Orion said:
I'd say it's whichever cities are owned by the faction's ruling clan at the beginning of the game, and in the cases where there are 2 (like Sargot and Galend) just pick whichever one the clan's leader hangs out in more.
I'm fairly certain someone curious could enable cheats and just teleport to each of the cities to see where different lord parties start, and deduce from there which cities are actually the de facto capitals