Enigmatic Engineering: Fallen Empire Ships
Yes, you read that right.
Ladies and gentleman, from the modder that brought you that one mod that let Enigmatic Engineering research all FE buildings AND ship components, give it up for:
Enigmatic Engineering: Fallen Empire SHIPS!!!
Now, what does this mod do, specifically?
Well, specifically, it overwrites the cosmogenesis ship techs, so that EE-taken empires can research them. This applies to both mechanical ships (Riddle Escort, Enigma Battlecruiser, Paradox Titan) and also the bio ships.
With that said, as you can imagine, this would conflict with any mod that overwrites these techs specifically. But you should probably be fine. Probably.
Best enjoyed with my other mod, Enigmatic Engineering: Fallen Empire Tech https://steamcommunity.com/sharedfiles/filedetails/?id=3514839896