I've noted when Thunder procs I can get it off almost exactly in time with my current FireI cast. Then go into the next FireI cast after the cooldown resets.

Seems to me that even though you have a chance for that FireI to proc it's better to get a half-casted spell off than interrupting it unless you'll pop the mob with it:
Each cast is an individual proc event. You're not "missing out" on a back-to-back except hypothetically. Even then It's less likely that Firestarter will proc again on that FireI than not.