I think in the Ellimist Chronicles it's stated at the end that Ellimist and Crayak are equal in power, neither would survive if it came to a fight between the two of them, that's why they play the game (Yay for the pawns!)
But I don't see how they're meant to criticize religion or even necessarily represent it, religions generally lay down rules for you to live by that would be of some benefit to you in this life or the next, the Ellimist doesnt have rules for others to follow but rather has rules for himself and Crayak to follow, and he doesn't seem super concerned with the next life, he's concerned with making sure that the current life goes on for as long as it can for sentient beings everywhere so he can sit back and watch life iteself do its thing like an old man sitting at a pond watching ducks.
And Crayak wants to destroy all life because . . . well, pretty much because he's mean and that's about as much explanation as we get. I guess he's the slightly older man throwing rocks at the ducks becaus they're making too much noise or something, so Ellimist says "calm down, let's play a game of chess or something." and Crayak says "Checkers or I throw more rocks!" and Ellimist says "Okay, okay, checkers, but with chess pieces."