That's one of the things I would like for what the Devs call "Emergent Story Telling". To paraphrase Star Trek's Dr. McCoy, It's history, but not as we know it.
It all goes Alternate History as soon as you un-pause the Game. People who die OTL, don't necessarily die this time around. Different Rulers, different genetics, and totally different outcomes.
Why shouldn't Rulers be able to build Cathedrals or Mosques in places where they weren't built OTL? And why forbid Rulers from building Universities anywhere if the have the Money, Prestige, and Piety to allows it?