I also do not really enjoy spells being tied to specific pieces of gear, however, I would take it over not getting the new spell at all.
If it can be put on an item it can be given to the player some other way. While Comet is an item exclusive spell, it is also a Fenrir blood pact and has the same effects. No reason not to just make a scroll for a spell like any other, at the very least some period of time after the special item.