It doesn't seem wonky to me to make a specialist add spells from their specialty school. After all, having spells in their specialty is part of what makes them specialists, no?
If you know all the core spells in your specialty when you are gaining your 2 spells for going up a level, you may learn a spell from any castable school, rather then being restricted due to your specialty. If their are core spells in your specialization that you do not know upon rising in level, you must apply 1 of the learned spells to a spell from your school.
The intent was to force specialists to act like them (an illusionist should know a lot of illusions). Since I do not believe the intent was to punish players who focused / learned their specialty school spells too efficiently, I'd opt for the above house rule - if no option exists in the used books, ignore the penalty.