Hi Nate,
like I wrote before - I'm not in front of my DAW these days, but writing from memory, you should be able to create so-called "child busses" in Cubase's "VST Connections", which allow for breaking up multi-channel signals in something like "front L/R", "surround L/R" and so on.
Another option would be to use a simple volume control plug-in in your Quad-channel, like Cubase's Surround Mixer Delay (... maybe this is a Nuendo-only tool?), or Vienna Suite Pro's Matrix Mixer.
Regarding MIR Pro's Secondary Mic: Like mentioned in the manual (and shown in the GUI), the Secondary Mic will indeed just return the wet signal from the room. MIR thinks very much along the lines of a recording engineer, who wouldn't use two spot mics for the same source in different angles and positions either. It would create an endless mess of phasing issues and wrong positioning cues.
... I completely understand what you're after technically, but please allow for the personal sidenote that it seems that you're overcomplicating things a bit. :-) MIR's signal flow actually tries to keep everything as simple as possible (... and still scares many people to death just by mentioning "virtual microphones" 8-) ... go figure), so maybe you should just give it a try and adopt to its "natural" workflow. ;-)
Kind regards,