This goes to the deity being worshipped under different names and guises. No matter what the deity does, all of the faith goes into a communal pool? It isn't possible to keep the Belief pools seperate?
You can track Belief however you want. We just lump it in for simplicity's sake. Our main goal is to make the player and Fate's tasks a little easier.
Can another deity 'stand in', and perform miracles and steal the Belief? Or do all such efforts only enhance the Belief of the founding deity?
Righto on the second part. It goes to the founding deity. There are no subsitutions.
Other than needlessly losing worshippers, are there any negative consequences of two different facades getting involved in a holy war with each other?
Not that I can think of, but the followers on both sides would like to know what the heck is going on. It should be a fun war to watch.