I'm also experiencing this bug with 2.3.3-RELEASE (amd64) using Unbound and no BIND. LAN (renamed "LAN1") serves regular workstation clients with the pfSense system domain (lan.mydomain.co.za) while I use OPT1 (I renamed to "LAN2") interface as a subnet for local servers (srv.mydomain.co.za -- only accessible from LAN1). pfSense DHCP server on LAN2 overrides domain name and domain search list correctly, and this works as far as DHCP clients and the server are concerned... but the corresponding automatic DNS entries (in Unbound) for non-static DHCP leases use the system domain suffix regardless.

To clarify: if I have DHCP client computer "foo1-pc" on LAN1 then pfSense correctly resolves its address from name foo1-pc.lan.mydomain.co.za. The problem is if I connect "foo2-pc" to LAN2 (also running DHCP client) then pfSense resolves foo2-pc.lan.mydomain.co.za but not foo2-pc.srv.mydomain.co.za

(side note, connectivity is not the problem here, just DNS entries pulled from DHCP table: foo2-pc correctly gets an IP address on LAN2 subnet and its DNS entry correctly resolves to said IP LAN2 address -- the problem is just the DNS entry is part of the LAN1 subdomain)

However, I found that static DHCP leases on LAN2 don't have this issue! Once a static lease is entered from Status -> DHCP Leases for foo2-pc its DNS entry is "foo2-pc.srv.mydomain.co.za". This solves my issue, since I was going to allocate static leases to all servers anyway. But the fact that new servers connected to LAN2 subnet will not show up on LAN2 subdomain until they are assigned static leases is a nasty surprise bound to come up again for the next admin.