My opinion
My best break down of the end of this movie is that John does accept the bowling shoes, but instead of showing that, he immediately moves into his idea of paradise. He gives the shoes to the girl he thinks needs them, making that right, he gets his money and goes back to square, making that right, he goes to the feds and they tell him in no uncertain terms to not worry about it, making that right, and finally get goes on a date with Grace and we find out he has an acting gig, making that right. Everything comes up peaches for him when Cowboy offers the shoes to paradise, so I have to believe that paradise was a practical thing and not some kind of goofy fairy tale ideal. As for Cowboy? Well thats still kinda stumping me, he appears to be an alien, but he could be God, dishing out redemption for people who are genuinely deserving. Neely could be a fallen angel? Neely has neck brace that would appear to indicate he's in the same boat as cowboy. The agent says he was dead in a dumpster, but nothing the agent said was really believable throughout. And the blue raincoat people...maybe they were angels too?
My biggest curiosity was the neck band-aids. Grace has one at the very beginning, John gets one when he wakes up after the whole desert deal, and the FBI agent has one as he walks out the door at the end. Now, if Grace AND John both were let into paradise, that would make sense because maybe for both paradise was each other, but why then the FBI agent? I kept thinking he was maybe another not-human character, but that still doesnt explain the band-aid. I will say, John asks him in the bar if Grace said where he'd be, but he said no, she lied to the FBI...so how did he find him? Everything about Kelsey Grammar doesn't quite jive as far as I can tell...its strange.