That's an interesting thought, but, as it is, it's only the EaW AI that doesn't seem to like them. In my experience, either EaW likes variants (ships) or it doesn't (hardpoints).The only other thing I can think of is that perhaps the EaW Star Base system doesn't like the "Variant of" system. Eventually I'm going to get around to trying that and renaming the Space Colonies back to the vanilla "(Faction)_Star_Base". But I'm kind of tested out right now from restarting PR like 50 times and waiting for 50 weeks to go by each time for the AI to take one planet...
Still, it's probably worth a test - did anything come of it? I know the AI's annoying, but you can delete the Pirate starting forces on the Core or something and it should engage the free grab behavior of the AI, which is essentially no-brainer attack mode.