It's normal for there to frequently be a few citzens following another religion within the holy city; unless there's so many doing so that the holy city doesn't have a majority of the religion there's no effect. (Minor exception of the follower policy yielding production per follower whose benefit maxes out at 15 citizens in the city following the religion). And I think it's Religious Unity reformation policy that could make that useful.
Now if some other religion is the majority religion then it's going to be that religion in which it externally influences. But holy city's also have internal religious pressure towards the religion founded in the holy city.
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