Here is what I do to check if things have improved after a change:
sudo /opt/dnscrypt-proxy/dnscrypt-proxy -service restart
sudo service dnsmasq restart
sudo apt-get update
The result:
Apr 27 10:02:49 dnsmasq[20851]: started, version 2.80test2 cachesize 65535
Apr 27 10:02:49 dnsmasq[20851]: compile time options: IPv6 GNU-getopt DBus i18n IDN DHCP DHCPv6 no-Lua TFTP conntrack ipset auth DNSSEC loop-detect inotify
Apr 27 10:02:49 dnsmasq[20851]: DNSSEC validation enabled
Apr 27 10:02:49 dnsmasq[20851]: warning: ignoring resolv-file flag because no-resolv is set
Apr 27 10:02:49 dnsmasq[20851]: using nameserver 127.10.10.1#5551
Apr 27 10:02:49 dnsmasq[20851]: using local addresses only for domain localdomain
Apr 27 10:03:00 dnsmasq[20851]: read /etc/hosts - 14 addresses
Apr 27 10:03:00 dnsmasq[20851]: read /etc/pihole/local.list - 2 addresses
Apr 27 10:03:00 dnsmasq[20851]: failed to load names from /etc/pihole/black.list: No such file or directory
Apr 27 10:03:07 dnsmasq[20851]: bad name at /etc/pihole/gravity.list line 471222
Apr 27 10:03:09 dnsmasq[20851]: read /etc/pihole/gravity.list - 601177 addresses
Apr 27 10:03:09 dnsmasq[20851]: read /etc/localdns.list - 39 addresses
Apr 27 10:03:09 dnsmasq[20851]: 1 127.0.0.1/37576 query[SRV] _http._tcp.archive.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: 1 127.0.0.1/37576 forwarded _http._tcp.archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: 2 127.0.0.1/46107 query[SRV] _http._tcp.raspbian.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: 2 127.0.0.1/46107 forwarded _http._tcp.raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: 3 127.0.0.1/55314 query[SRV] _http._tcp.raspbian.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 dnssec-query[DS] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 dnssec-query[DNSKEY] . to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 reply . is DNSKEY keytag 19036, algo 8
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 reply . is DNSKEY keytag 39570, algo 8
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 reply . is DNSKEY keytag 20326, algo 8
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 reply org is DS keytag 9795, algo 7, digest 1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 reply org is DS keytag 9795, algo 7, digest 2
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: 3 127.0.0.1/55314 forwarded _http._tcp.raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 dnssec-query[DS] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37576 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 dnssec-query[DNSKEY] . to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20929]: 103 127.0.0.1/55322 query[SRV] _http._tcp.archive.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply . is DNSKEY keytag 20326, algo 8
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply . is DNSKEY keytag 39570, algo 8
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply . is DNSKEY keytag 19036, algo 8
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply org is DS keytag 9795, algo 7, digest 2
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply org is DS keytag 9795, algo 7, digest 1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20929]: 103 127.0.0.1/55322 forwarded _http._tcp.archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply org is DNSKEY keytag 17883, algo 7
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply org is DNSKEY keytag 1862, algo 7
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply org is DNSKEY keytag 9795, algo 7
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply org is DNSKEY keytag 6368, algo 7
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply raspberrypi.org is DS keytag 49776, algo 10, digest 2
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply raspberrypi.org is DS keytag 24957, algo 10, digest 2
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 dnssec-query[DNSKEY] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply org is DNSKEY keytag 9795, algo 7
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply org is DNSKEY keytag 17883, algo 7
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply org is DNSKEY keytag 1862, algo 7
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply org is DNSKEY keytag 6368, algo 7
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply raspberrypi.org is DS keytag 24957, algo 10, digest 2
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply raspberrypi.org is DS keytag 49776, algo 10, digest 2
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 dnssec-query[DNSKEY] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply raspberrypi.org is DNSKEY keytag 33908, algo 10
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply raspberrypi.org is DNSKEY keytag 49776, algo 10
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply raspberrypi.org is DNSKEY keytag 24957, algo 10
Apr 27 10:03:09 dnsmasq[20928]: * 127.0.0.1/55314 reply raspberrypi.org is DNSKEY keytag 23675, algo 10
Apr 27 10:03:09 dnsmasq[20928]: 3 127.0.0.1/55314 validation result is SECURE
Apr 27 10:03:09 dnsmasq[20851]: 203 127.0.0.1/37852 query[A] raspbian.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: 203 127.0.0.1/37852 forwarded raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: 204 127.0.0.1/37852 query[AAAA] raspbian.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: 204 127.0.0.1/37852 forwarded raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37852 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply raspberrypi.org is DNSKEY keytag 49776, algo 10
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply raspberrypi.org is DNSKEY keytag 23675, algo 10
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply raspberrypi.org is DNSKEY keytag 33908, algo 10
Apr 27 10:03:09 dnsmasq[20929]: * 127.0.0.1/55322 reply raspberrypi.org is DNSKEY keytag 24957, algo 10
Apr 27 10:03:09 dnsmasq[20929]: 103 127.0.0.1/55322 validation result is SECURE
Apr 27 10:03:09 dnsmasq[20851]: 205 127.0.0.1/33024 query[A] archive.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: 205 127.0.0.1/33024 forwarded archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: 206 127.0.0.1/33024 query[AAAA] archive.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: 206 127.0.0.1/33024 forwarded archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/33024 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37852 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/33024 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20931]: 207 127.0.0.1/55338 query[A] archive.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37852 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: nameserver 127.10.10.1 refused to do a recursive query
Apr 27 10:03:09 dnsmasq[20851]: nameserver 127.10.10.1 refused to do a recursive query
Apr 27 10:03:09 dnsmasq[20932]: 307 127.0.0.1/55342 query[A] raspbian.raspberrypi.org from 127.0.0.1
Apr 27 10:03:09 dnsmasq[20851]: * 127.0.0.1/37852 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20851]: 203 127.0.0.1/37852 reply raspbian.raspberrypi.org is <CNAME>
Apr 27 10:03:09 dnsmasq[20851]: 203 127.0.0.1/37852 reply mirrordirector.raspbian.org is 93.93.128.193
Apr 27 10:03:09 dnsmasq[20931]: 207 127.0.0.1/55338 forwarded archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20932]: 307 127.0.0.1/55342 forwarded raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20932]: * 127.0.0.1/55342 dnssec-query[DS] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 reply org is DNSKEY keytag 9795, algo 7
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 reply org is DNSKEY keytag 17883, algo 7
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 reply org is DNSKEY keytag 1862, algo 7
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 reply org is DNSKEY keytag 6368, algo 7
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 reply raspberrypi.org is DS keytag 49776, algo 10, digest 2
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 reply raspberrypi.org is DS keytag 24957, algo 10, digest 2
Apr 27 10:03:09 dnsmasq[20931]: * 127.0.0.1/55338 dnssec-query[DNSKEY] raspberrypi.org to 127.10.10.1
Apr 27 10:03:09 dnsmasq[20932]: * 127.0.0.1/55342 dnssec-query[DNSKEY] org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20931]: * 127.0.0.1/55338 reply raspberrypi.org is DNSKEY keytag 49776, algo 10
Apr 27 10:03:10 dnsmasq[20931]: * 127.0.0.1/55338 reply raspberrypi.org is DNSKEY keytag 33908, algo 10
Apr 27 10:03:10 dnsmasq[20931]: * 127.0.0.1/55338 reply raspberrypi.org is DNSKEY keytag 23675, algo 10
Apr 27 10:03:10 dnsmasq[20931]: * 127.0.0.1/55338 reply raspberrypi.org is DNSKEY keytag 24957, algo 10
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 validation result is SECURE
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply archive.raspberrypi.org is <CNAME>
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.130.39
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.130.104
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.130.214
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.135.188
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 46.235.227.11
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.128.133
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.128.211
Apr 27 10:03:10 dnsmasq[20931]: 207 127.0.0.1/55338 reply lb.raspberrypi.org is 93.93.128.230
Apr 27 10:03:10 dnsmasq[20931]: 208 127.0.0.1/55338 query[AAAA] archive.raspberrypi.org from 127.0.0.1
Apr 27 10:03:10 dnsmasq[20931]: 208 127.0.0.1/55338 cached archive.raspberrypi.org is <CNAME>
Apr 27 10:03:10 dnsmasq[20931]: 208 127.0.0.1/55338 forwarded archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20931]: * 127.0.0.1/55338 dnssec-query[DS] archive.raspberrypi.org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply org is DNSKEY keytag 6368, algo 7
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply org is DNSKEY keytag 1862, algo 7
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply org is DNSKEY keytag 9795, algo 7
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply org is DNSKEY keytag 17883, algo 7
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspberrypi.org is DS keytag 49776, algo 10, digest 2
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspberrypi.org is DS keytag 24957, algo 10, digest 2
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 dnssec-query[DNSKEY] raspberrypi.org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20931]: * 127.0.0.1/55338 reply archive.raspberrypi.org is no DS
Apr 27 10:03:10 dnsmasq[20931]: 208 127.0.0.1/55338 validation archive.raspberrypi.org is BOGUS
Apr 27 10:03:10 dnsmasq[20931]: nameserver 127.10.10.1 refused to do a recursive query
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspberrypi.org is DNSKEY keytag 33908, algo 10
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspberrypi.org is DNSKEY keytag 24957, algo 10
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspberrypi.org is DNSKEY keytag 23675, algo 10
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspberrypi.org is DNSKEY keytag 49776, algo 10
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 dnssec-query[DS] raspbian.org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspbian.org is no DS
Apr 27 10:03:10 dnsmasq[20932]: 307 127.0.0.1/55342 validation result is INSECURE
Apr 27 10:03:10 dnsmasq[20932]: 307 127.0.0.1/55342 reply raspbian.raspberrypi.org is <CNAME>
Apr 27 10:03:10 dnsmasq[20932]: 307 127.0.0.1/55342 reply mirrordirector.raspbian.org is 93.93.128.193
Apr 27 10:03:10 dnsmasq[20932]: 308 127.0.0.1/55342 query[AAAA] raspbian.raspberrypi.org from 127.0.0.1
Apr 27 10:03:10 dnsmasq[20932]: 308 127.0.0.1/55342 cached raspbian.raspberrypi.org is <CNAME>
Apr 27 10:03:10 dnsmasq[20932]: 308 127.0.0.1/55342 forwarded raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 dnssec-query[DS] raspbian.raspberrypi.org to 127.10.10.1
Apr 27 10:03:10 dnsmasq[20932]: Insecure DS reply received, do upstream DNS servers support DNSSEC?
Apr 27 10:03:10 dnsmasq[20932]: * 127.0.0.1/55342 reply raspbian.raspberrypi.org is BOGUS DS
Apr 27 10:03:10 dnsmasq[20932]: 308 127.0.0.1/55342 validation raspbian.raspberrypi.org is BOGUS
Apr 27 10:03:10 dnsmasq[20932]: nameserver 127.10.10.1 refused to do a recursive query
Sometimes, I even get (on the pi console):
sudo apt-get update
Err:1 http://raspbian.raspberrypi.org/raspbian stretch InRelease
Temporary failure resolving 'raspbian.raspberrypi.org'
Hit:2 http://archive.raspberrypi.org/debian stretch InRelease
Reading package lists... Done
W: Failed to fetch http://raspbian.raspberrypi.org/raspbian/dists/stretch/InRelease Temporary failure resolving 'raspbian.raspberrypi.org'
W: Some index files failed to download. They have been ignored, or old ones used instead.
In the mean time, I'm still continuing my conversation with the dnsmasq developer.