I think there should be spells unique to a single town (or a pair of towns).
Example: the mass murder-death-kill spell that is one of the 5th level dark magics should be available only to the necropolis and inferno, maybe dungeon, but especially not to haven or sylvan.
Should there be restrictions on which spells a town can have?
I think there are enough restrictions: You have to be proficient in that particular school in order to cast level 3-5 spells. That's enough restriction for me. I have no problem with making Mastering of certain classes Faction dependant (as in my other post), but no more than that.