Took me a while to notice, and more to diagnose, but the ufocontents asset folder is creating some odd effects. For one, despite the contents of those files clearly indicating there should be variation in the units, all I'm getting are soldiers of some kind - every. single. battle. But it also seems to be placing the aliens unusually close to my dropship (occasionally 5-10 squares out) and *never* in the UFO - not once in quite a few battles. I'm guessing it's resorting to random placement instead of using the map settings.. I've tested this with all map packs removed and a vanilla game with nothing but CE applied.
This becomes game breaking for new games, as it effectively removes noncombantant aliens, meaning no plasma pistol, meaning dead end for research.
Removal of this folder seems to fix the issue, and I'm not seeing any problems as a result of that. Given the difference in how the data is represented between the original and modded xml files, I'm thinking there's a bug in how it's reading that data in.