You're correct that the tunneled server is not the default gateway – I do serve tunneled DNS via DHCP but I also have failovers, that way if the tunnel ever goes down users under the "client" pfSense box will still be able to access the internet, just not the LAN bridge.
Thought it might be a NATting issue of some kind. I did opt for box #2, as the ClearOS server is a VM in and of itself. I could go through the nightmare of connecting it via a vSwitch with specific routing instructions but since it's all internal and behind several firewalls on both ends of the tunnel anyway, I think it'll be fine. For the intended bridging purpose, it's not the end of the world that all tunneled requests will appear to come from the "server" pfSense VM.
Thanks for the concise and helpful assist. Works perfectly now. +1 to viragomann