I've got a similar problem. My install is far more heavily modded than that (~25 mods), though, and the DLCs I bought didn't include Supremacy. I went with Celestial Worlds and Untold Tales instead.

It started off with that same type of critical error when I tried to play the new expansions without mods, and according to the resulting error report, this was caused by the game trying to load assets that were associated with the mods I'd deactivated, failing to do so, and resultingly failing to load. It happened several times, which is why I checked the error report in the first place (the one that loads in a web browser for some reason). So I turned on my mods again, got the game to load, started a new custom faction and a new game, and... all the AIs turned into Sophons. They weren't set to Sophons, but that's what they ended up.

I'd also encountered a severe endgame error - I conquered all of the space outside my alliance's territory, had achieved what should've been a wonder, economic, and possibly research victory a long while before that, and couldn't win. It was just me and the remaining Sophons sitting around waiting for nothing to happen.