Coming back to DNS forwarder not resolving local (fully-qualified) hostnames after upgrade from 2.3.2_1 to 2.3.3_1, it turns out this was caused by:
I had the same issue, not even long domain names worked in the DNS forwarder.
Turns out it is due to a setting in the General Setup "DNS Server override"
"If this option is set, pfSense will use DNS servers assigned by a DHCP/PPP server on WAN for its own purposes (including the DNS Forwarder/DNS Resolver). However, they will not be assigned to DHCP clients."
That was checked on my setup and as such none of my local - full domain forward overrides - worked anymore.
This was never a problem before pfSense 2.3.3_1.
Perhaps it makes sense, but at least unchecking that and manually setting the DNS server setting above that instead of getting it from DHCP immediately fixed the issue I was having.
After that I could query for any of the internal DNS entries again.
Thanks to @wila (https://forum.pfsense.org/index.php?action=profile;u=320599)