On the latest TA beta.
I have no idea if this was an issue in the past with DA or DL but I never ran into it.
Played a game as the Arceans and had many custom ships. Example might be "Defender M2".
In my current game as the Korx I have tried to create a custom ship and also call it "Defender M2" and it gives me the warning that you shouldn't name a new ship the same name as a current custom ship name.
Sooo, I had always thought that the custom ship files were race specific or at least ship style specific, but I guess they aren't? If they aren't then I think that should be a feature in TA that custom ship names don't conflict between races or ship types from game to game.