I've assumed that the dev team would want there to be a default natural progression for every civ, so that when you play a full game, there's actually a chance of seeing every civ. If there isn't a default route, then those civs are unlikely to appear as an opponent in single player games without an advanced start. As ugly as it is, I don't know which Antiquity era civ would lead into Spain (given that Rome would already be taken) other than the Maya. The same for Meiji Japan - Siam is a much nicer choice for something coming originally from Khmer, but then I have no idea where Japan would go.
It might just be that the devs don't care too much if some civs are unlikely to appear in the game, or if some civs have no default paths and are chosen entirely at random on era progression.