In PF2e, the specific gods and factions of the default setting are actually integral to the game’s mechanics, which makes it a lot harder to play the system in a homebrew setting
Ehhh. You can ignore a lot of the setting specific stuff, especially with the remaster. I just let clerics choose their own edicts and anathema, and favoured weapon, for instance. It's not like the actual lore of the gods matters to the game mechanics. You can build gods or sects piecemeal.
Or don't. My family's game has both a cleric and a champion, neither of which has a specific god. They're just "good". It works just fine.