The drow did get "whitewashed" somewhat as of 4e, if I am not mistaken, as many of them were driven to the surface during the Spellplague events and there was a whole diaspora living in at least Neverwinter.
I do agree that the githyanki should just have a different BG city experience in Act 2 from the rest of the races. You see a Flaming Fist patrol wiped out by them, and being all welcome in a city that seems to be going through crises on a regular basis in the late XVth century as an outer-planar usually-invader whose people have no concept of empathy would be really out of place. I guess there could be deception checks involved to try to pass oneself as a githzerai or something (and a githzerai would have to do persuasion checks to convince people that they aren't dangerous).
