Custom dnsmasq.d rules should be fine. No difference between regular pihole really, other than the files are volume mounted in from my workspace so pathing is `./etc-dnsmasq/ points to /etc/dnsmasq.d/.
I just tested this with one of my external domains to confirm it worked:
# Before edit
$ host techjunktrunk.com
techjunktrunk.com has address 104.28.25.19
techjunktrunk.com has address 104.28.24.19
techjunktrunk.com has IPv6 address 2606:4700:30::681c:1813
techjunktrunk.com has IPv6 address 2606:4700:30::681c:1913
techjunktrunk.com mail is handled by 10 mail.protonmail.ch.
# Edit the volume mounted directory / config
$ vim etc-dnsmasqd/02-diginclan.conf
$ grep techjunktrunk etc-dnsmasqd/*
etc-dnsmasqd/02-diginclan.conf:address=/techjunktrunk.com/192.168.9.99
# Bounce container/dnsmasq
$ docker restart pihole
pihole
# Updated (my computer's DNS points to the pihole also)
$ host techjunktrunk.com
techjunktrunk.com has address 192.168.9.99