This might be hardcoded into M2TW due to building tree complications, but if it's not it should be reverted. Churches and mosques should stay on the battle map of cities regardless of the faith of the faction owning the settlement. It's stupid and unhistorical to have it otherwise, given the enormous quantity of Christian churches that were converted into mosques and the other way around: Islamic mosques that were converted into churches throughout the ages. Prominent examples include the Hagia Sophia in Constantinople being turned into an Ottoman mosque, or the Moorish Mosque–Cathedral of Córdoba turned into the Castilian/Spanish Cathedral of Our Lady of the Assumption (Spanish: Catedral de Nuestra Señora de la Asunción). It would have been retarded to knock these buildings down and establish new ones when it was simply cheaper and easier to re-purpose them.
M2TW the game and all its mods, however, FORCE you start building tiny churches from the ground up, until you've spent a billion dollars making the cathedral and then huge cathedral again.
I mean, come on: a medieval European city without a cathedral in its skyline would be like a car without an engine, a sandwich without meat, or a supermodel without breasts.
For that matter, another stupid thing: Orthodox churches and cathedrals don't appear on the battle map. That's something at fault with the original vanilla M2TW, but it's something modders have never corrected, for some odd reason. Seems like a no-brainer to make custom Orthodox churches or simply use existing church models.
There are really simple solutions to this problem, actually, and Europa Barbarorum II (EB II) for M2TW has proven it. The antiquity mod De Bello Mundi (DBM) had settlements with the exact same problem only it involved custom ancient polytheistic temples (with models taken from original Rome Total War cities). EB II fixed this problem by permanently placing the temple type building in cities, large cities, and huge cities. It didn't matter if the campaign map building tree contained a temple or not, or a small temple or large temple: the same temple model appeared in every minor city, and the same was done for every large and huge city.
This is a viable solution for Stainless Steel 6.4. Islamic cities should still have their mosques and jamas after pagan, Orthodox or Catholic factions conquer them, and the Christian factions should still have their churches and cathedrals.