Current Sub Rosa #21 Heaven and Hell tackles interaction with the Church, religious characters and religion in general head on - and you can see from the reviews here, how deeply ingrained the avoidance of these topics in several sagas is.
So your question is indeed not rhetorical at all.
Going beyond the denial/avoidance of religious issues in a saga in a way truely respectful to the historical faiths involved requires first and foremost a solid research.
Relying on the necessarily limited treatment in the role-playing game proper limits you indeed to the dominant religions in 1220 Mythic Europe and surroundings, and to their more common features. Blaming ArM5 for this is just disingenuous.
Every saga needs to decide its limits here on its own: especially when the differences between historical and contemporary faiths come up, of which David Chart wrote in his From the Line Editor in Sub Rosa #16: "Even this approach presents difficult issues. The immediate issue that prompted someone to call me an anti-Catholic bigot was my presentation of an aspect of theology, which, I was told, was obviously from a Protestant polemicist. In fact, it was taken directly from St Thomas Aquinas."
I personally prefer to candidly address these as well. I expect, that role players in Mythic Europe are prepared to accept and explore in-game not only a different world than their own, but also the historic faiths that come with it.