While not exactly at the start of the game, early on when you had to pick your sub faction in game apparently you got some bonuses and penalties for picking each sub faction. But that's been removed and despite several long threads to the contrary it probably won't be happening.

That said, I already have a mod that does this for trinity and faction uniqueness will be the first big thing I'll adjust, mostly with starting faction bonuses. So if you mostly play single player at least it won't be a huge deal...