I fear that in many places, you will see two different realms each with their own state religion declares their respective realm good when they are allied to have their priests help each other, even though they do not share a faith. Priests would be like glorified courtiers that can work inter-realm.... I prefer the current system where the actions are only determined by number of followers, not realm allegiance.
I think you are missing the broader implication here. This (and many of the other new proposals) would make larger religions more powerful. Powerful enough that
if you were inclined to do things strictly by the numbers as you see above, then you would decide you needed just one religion between the realms. And if you didn't, you would be at a significant disadvantage.
