I must confess I've never really tried using modded wads before but I have managed to get Aliens TC working under Chocolate Doom for win32 this week just to see how it works. Seriously impressive stuff, way better than I was expecting!
It shouldn't be a major hassle to get this working in Dooom, so I'll try and add it for the next release. I've been a bit distracted lately as I managed to get CaSTaway working on Native a couple of weeks ago and I've been playing with that since!
I've been adding back the dehacked support for modded wads and am hopefully not far off getting something working, just sorting out a problem with the merging process. The good news is the weird enemy behaviour was being caused by the removal of the dehacked stuff so this is fixed now, all the demos play back perfectly which is really nice to see!