It's possible. Like I said he's kind of a casual... Arceist? So he'll just nr thinking these radicals need to chill out. But at the same time anyone who's trying to worship anything other than Arceus is obviously wrong in his eyes. In the same way that you'd react to someone saying the sky is green and the sun rises in the west.

Which is funny cause this is a world where their gods can literally duke it out. 

Wonder where atheists would fit into all of this. Just go around claiming that Arceus and Rayquaza are just Pokemon. They didn't create anything. Actually in that sense they may tolerate worship of Rayquaza since it's a sort of protector and not a "God". But now I'm rambling and since I'm on my phone I can't go back and check again on what you said about Rayquaza in the OP so I'll put off thinking about it for now.