This thread just makes me want to incorporate my old Arkhan'a religion into BM even more. 
Based off of Greek, Norse, Sumerian and Egyptian mythology with a few interesting twists, the religion itself is rife with rivalry. Every follower respects each of the pantheon's deities, yet like in many ancient polytheistic nations, individual nations, regions, and city-states tend to favor one god or goddess over another.
This is basically AP. Admittedly I did focus more on Slavic, Germanic, Uralic and Greco-Roman mythologies, plus some Shintoist influence, but it is also intended to be open ended, so that anyone that wants to add into the mix is able to. Each noble has its own deities with which he has a "blood" relationship (from whose's essence his soul was made of), and naturally favors. Besides those whose relationship with the divine goes through more shamanistic traditions.
Hell, my entire proposed 3-part Fantasy novel series was effectively the war of the gods utterly f*cking the world to the point where mortal kind had to choose sides, which others went so far as to aspire to destroy the gods themselves. (With the help of certain ambitious and devious gods willing to trick mortals into becoming their champions, effectively recruiting living weapons with which to fell their own kind in their covetous desires. 
)
That is interesting, and I had envisioned something quite alike: each god in AP serves its own purposes, which usually conflict with each other, but they were (and are) sort of forced to cooperate to create and maintain our world (for more info on why see our creation myth). While aspiring to destroy the gods would be madness (like an ant aspiring to destroy the sun), the presence of other kinds of spirits (not necessarily benign to us) dwelling both in the spiritual and mortal worlds sort of matches your last phrase.
Of course there is a lot unsaid, and that is completely intended, for no god or priest who serves him would likely spill out the whole truth when it might work against him.
That said if you decide to create such kind of religion it would be awesome. The interaction between our two cults and characters would probably render very fun RPs.
