I just checked Kay's Attribute points again, and I'm an idiot. In fact, I think Kay has extra Attribute points, so I retract that part completely. The part about her low VP stands, though.
For some reason, Kay starts with half the VP and one fewer Attribute point than she should. Her stats are all the same as Bastila's, but Bastila starts at level 3 while Kay starts at level 6. This means she misses out on 3 levels' worth of VP and the Attribute point at level 4.
Otherwise, the mod seems to work very smoothly, although at this point I've just recruited Kay. I haven't gone through the whole game with her yet.