Struggling with pihole-FTL

No, more details below.

They aren't. The web interface calls the CLI which edits /etc/dnsmasq.d/01-pihole.conf and restarts pihole-FTL afterwards.

You can find this here:

becoming effective here:

You can pass your options to the embedded dnsmasq using

pihole-FTL -- -v

If this tells you that the log file is not writable (because you invoke FTL as the wrong user), use either

sudo -u pihole pihole-FTL -- -v

or chown the file momentarily