I agree for most big religions this would be the case, so I can see why changing the main game to be individual-based would be a little fraught. Cults, however, are a different story, since they often really do have just a few members whose beliefs change over time. I think the-blind-ones system would work really, really well for that. It would definitely be a good mod, but playing as a preestablished religion, it doesn't work as well.
Making the traits into individual precepts is really interesting to me though. I think the way that ideology handles individuals sinning (assuming it was forced, having the pawn take a mood debuff) is a little wacky since people willfully go against their religion all the time. Making nudist/cannibal etc. negate those precepts is a step in the right direction, and maybe general traits like "devout" or "fake believer" would help, but having individual precepts which can be slightly different from the main ideology works too.
Making the traits into individual precepts is really interesting to me though. I think the way that ideology handles individuals sinning (assuming it was forced, having the pawn take a mood debuff) is a little wacky since people willfully go against their religion all the time. Making nudist/cannibal etc. negate those precepts is a step in the right direction, and maybe general traits like "devout" or "fake believer" would help, but having individual precepts which can be slightly different from the main ideology works too.