Similar to modding planets, I find that modding in new ships is something that I need to do frequently. While my current solution around this is to do some jankery with ship textures and alternate skins, having additional duplicates of faction ships similar to how we use the same method to create planets would allow modders such as myself to create new factions with their own ships without messing up another faction's ships. I'm not sure how much work this would involve, but hopefully it's minimal enough to include in the next patch.

Also I once again request AI and Quest modding documentation, though seeing how ES2 doesn't have a many people on it anymore, I'm not expecting an answer.