It's a good attempt at faction differentiation, but not so good an implementation of it, imho.
You don't see complains of the type "I cannot get Green Thumb during the game" or "I cannot get Attunement" during the game. Like Talents/Weaknesses and Professions, those spellbooks are one time deal. You pick them or not, much like Green Thumg, Stupid or Royalty. Only things you can actually research that can also be bought during Sov creation is equipment.
About default Sovereigns, they are as they are. The fallen Sovereigns' talents/weaknesses seem quite "lets give them something" to me. And spellbooks are given as... whichever the reason. But that's not reason enough to say "I should be able to research the books from Sovereign creation".
Differentiation? According to the Hiergamon (the book, not the web thing), Procipinee seems to be the only human Sovereign able to revive the lands. Not that in game seems to mean anything at all right now, but would indicate that if the default Sovereigns were to get really deep in their differentiation, it would include also access to exclusive spellbooks (or just spells?).
I want to think that for Expansion 2, the factions will really be different (looking for equivalents to Gal Civ II).