I found something that could explain everything when I mixed every dumb theory.
Bret Stiles gang banged the aunt of Van Pelt, then every spermatozoon fused all their DNA and produced a superpower psychic abandoned to a con father at circus.
But his Evil Plan didn't work and he turned out to be a wonder boy.
Then Bret tried again and Red John was born with a little more consanguine farmboy's sperm.
That could be explain everything :
Red John could be a twin, a father, a son, a daughter, a brother, a sister, all at once, and he can fits every stupid theory you are making.
He can even easily fake his death apparently it's a common thing to do when you are a common smart psychopath.