Yeah, sometimes you really have to tilt your head to make the story make sense.
NWN II is the same way. The Mask of the Betrayer expansion really only makes sense if you chose the good ending. Going evil at the end of NWN II... well it ends radically different. At the same time though, the expansion makes zero sense starting with a new char. Then again, with fantasy games it's generally easy to just think of some sort of divine intervention/magic/
aliens to explain the discontinuities. An active role is sometimes needed in filling in the holes. Or even the entire story-line, heh.