Yes, the civilizations can be overriden via a civilizations.json file.
See:
So long as the number of civilizations defined in the data mod matches the number of civilizations in the civilizations.json file, the mod should work.
Assuming you have all but the latest 3 civilizations in your mod, you can copy the base game’s civilizations.json file to your mod’s dat folder and remove the 3 new civilizations from that file.