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.
Fair points, though I would say my own criticism of the divine 5e (which is pretty mild as I think it mostly is a great take on a difficult topic) is mostly due to difficulties I've had being someone who is willing to go out and do the research (and enjoys it) with reconciling trying to do the less prominent faiths justice with the way the divine is presented.
I very much like the rules in RoP:tD etc. I just think with some tweaks to how things are framed when the divine is introduced could offer more freedom to develop less prominent faiths for those that want to without needing any increase in complexity for those that are happy with the major faiths or with avoiding the divine altogether.
On that last note I myself was accused (privately) of anti-Catholic sentiment because of things I posted in this very thread (a remark about medieval Christianity being fairly close to de-facto polytheism, from a certain point of view). That was certainly a new one to me, as I'm a Catholic! Although in hindsight I can see how it could have been taken the wrong way.
We had this issue in my troupe in the past. We tended to play in Catalonia (our real world home turf) until PRECISELY these issues made us move to other foreign tribunals (brit isles and the far north).
In the end we decided that most monotheistic religions were wrong. All of them got the basics right, but later the trappings of secular power and influence (and the need to codify everything of humans) added a lot of crap to it. So Muslims, Christians and Jews got it right. Sol invictus does not, and neither do the cathars. The cathars talk real bullshit here, with the world being created by the demon, and that is just wrong. their prefecti can have mystical power, but it will be of an infernal nature because they have an inherent and unavoidable sin: that of hubris thinking they are better than their peers (souls about to Ascend). the PLAYERS decided this. the MAGI are totally unsure about it since Hermetic magic has no way of differentiating between divine and infernal magic. Cathars were a friendly faction in a lot of adventures.
Having the major religions getting it right does not mean that a Christian feels at pace in a mosque. He does not because he as a strong cultural bias. True faith does not prevent that bias. Relativism does not work well in our Mythic Europe. reading you all this can easily be inconsistent. It has never bothered us, though.
Other religions have not been thought much about except that the old religions tend to be associated with beings of power, like they do in the current setting.
But as others point out, we try to keep the sagas religion.lite in terms of doctrine. Religion is everywhere, just handwaved.