That is correct and expected.
Pi-hole blocks those requests by intention.
DNS lookups would defeat the Tor network's decentralised operation.
.onion domains are not meant to be resolved via DNS.
Quoting from RFC7686:
- Caching DNS Servers: Caching servers, where not explicitly
adapted to interoperate with Tor, SHOULD NOT attempt to look up
records for .onion names. They MUST generate NXDOMAIN for all
such queries.
and:
- Authoritative DNS Servers: Authoritative servers MUST respond to
queries for .onion with NXDOMAIN.
NXDOMAIN is the required reply, and the respective entries from 06-rfc6761.conf will have Pi-hole serve that reply immediately, instead of needlessly involving an additional roundtrip to its upstream servers, while preventing unintended .onion leakage at the same time.
EDIT:
You surely can configure Pi-hole for your use case, and you don't need to edit 06-rfc6761.conf for that.
Create a custom configuration file (e.g. /etc/dnsmasq.d/42-onion-forwards.conf) with:
server=/onion/<ip.ad.re.ss>#<port>
Substitute <ip.ad.re.ss>#<port> with the respective values for your Tor proxy and run pihole restartdns to apply.