Actually, from what I've been able to determine, that isn't the case. The character uses the current class bonus (i.e., the one the latest level was taken in), and not the best of the two.
I reverse-engineered the stats in the back for Luke, Han, and other movie characters. IIRC, Luke only had a +2 to his Defenses across the board. If he "kept the best and ignored the rest," then he would've had a +4 in one of the stats (due to the levels in Ace Pilot) instead of just the +2 for Jedi Knight (I think Reflex, but I can't recall which for certain).