In the expansion pack, Alpha Centarui: Alien Crossfire there were 2 alien factions alongside the usual human factions. If the aliens or humans took a base from the other, the base was reduced to 1 population, and the rest of the population took flight in colony pods. This represented the two species being so radically different that there was no possible way at coexistence within a single base.
I would consider this the baseline, and then if we want to get creative with coexistence, hybrid cities, etc. we can hash that out.