Chaosmancer
Legend
It would be other than the fact there is not one single church to form such a Theocracy. There are literally hundreds of different faiths, all of which are competing against each other.
Some societies are de facto or de jure Theocracies; the ones where the members of the faith of a single God has eliminated all rivals (the Zentarim and their worship of Bane is a good example). The Mulhorandi have united under a loose pantheon, and the Untheric nation did the same.
I guess my quick writing was a bit of a mistake.
When I said that "the world would be a Theocracy" I meant that every country would be a Theocracy, not that they'd all be the same Theocracy.
Assuming that doesn't clarify, I'll move on to assuming that you are referring to the number of churches in existence would mean that Kings would still rule. I think that is completely wrong.
Looking at historical records of places like Babylon or Akadia, heck even Egypt, we see that even with multiple competing dieties and religions, a stable government was able to form, with the Ruler also being a High Priest of a religion. I would also say that a Republic run by a group of churches still qualifies as a Theocracy. It would just be a Theocratic Republic.
Amusingly, this would actually work incredibly well in FR, considering how many of the "nations" of FR are really just City-States. That organization would be perfect for a set-up where local churches take power, bullying the other religions into lesser positions of power.
But, back to the broader point. If the solution to "why isn't everyone in FR dead from all these catastrophes" is "the churches work miracles to keep everything running" then that should logically lead into "the churches run everything"
It doesn't though. As you mention, Theocratic societies in FR are actually rare, which does not follow from the set-up. Sure, maybe one or two incredibly good political figures could play the churches off each other to balance themselves at the top of the heap, but if your biggest political question is "how do I ensure the church's loyalty" we are working in a very different world than what is presented.