You might think it was balance but really think it was more to be thematic, perhaps even channeling AD&D specialization where you choose to excel in one school (such as conjuration) but can't use any of the opposing school such as alteration (root).
I don't think was based on any other logic. Look at SKs for instance. Necromancers have better roots over their career than clerics but for some reason SKs can never even figure out to cast the first level root, yet paladins get several of that spell line.
And they mainly were expecting people to group primarily, not solo, so didn't focus on balancing for solo play.
Hybrid exp penalty thing is straight out of AD&D too and also wasn't properly balanced.
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