Yes religious conversion is ahistorical due to how fast it happens.
Most Orthodox provinces remained orthodox during EU IV's period, Shia provinces remain so to this day and is the source of great conflict in the middle-east, Protestantism doesn't spread far enough and is easily countered.
The system is arcadey so people can get a silly one faith achievement

.
I doubt they will change it, at heart vanilla EU IV mechanics are skewed in favor of aggressive expansionism, blobbing and world conquest in a period were this never happened because a strata of EU IV players love this kind of gameplay and they are the most vocal.
Paradox has tacked on blob nerfs over the years, corruption, state limits etc... but they are overall badly received by the WC/blobbing fans.
Everything happens too fast for the player: Colonization (especially in Africa), religious conversion, coring, army professionalism; I mean standing armies weren't a thing before the 1610s in Sweden and 1640s in Western Europe yet I can get "salaried soldiers" by the 1460s and "regimental mustering" by the 1510s at the height of the Condotierri Age, how ironic.
Even the most sluggish one, culture conversion is quite fast compared to the real world. I don't think Sicilians felt Spanish back in the 1600s, and I don't think they consider that period under Spanish Hapsburg dominion part of their cultural heritage. I mean they weren't truly Italians until early 20th century...
Of course the AI tends to lag a bit compared the player when dealing with all of the above and they are especially lousy colonialists, notably in the Americas.
I mean they take ages to start colonizing and don't even do so logically along their respective trade streams (i.e France going for Mexico, England for Colombia while Portugal owns the Caribbean and Spain Brazil, USA and Canada no one cares besides Norway or Scandinavia....)
Thing is by
slowing things down, you make the game less fun, because as I said before at it's core E.U IV is a game about blatant and ridiculous expansionism and blobbing.
They can't just slow religious conversation or colonization down without making said mechanics more engaging, active and fun. If we are going to wait that long for conversions, coring or colonization to happen we need more dynamic events, revolts and management to do in peacetime.
Sure all the above irks historical OCD, pro railroading players like me but oh well, I still love this game, cuz it's way more historical than the civilization series.
So, food for though for EU V.
Cheers all, sorry if it was a bit ranty and off-topic