I guess it's possible that Flea is just a really crazy girl who deludes herself into believing that she's a guy. Frog doesn't argue with it or act surprised when Flea declares his manitude, though, and since Frog knows best when it comes to Magus & Company, I'd go with it.

For a minute, years ago, I, too, thought that maybe Ted Woolsey just couldn't think of a good female musician after which to rename Mayonnaise, so he went with Flea and just wrote in that part about Mayonnaise being a guy in order to be consistent with the real Flea's gender. I quickly caught myself, however, as the chances are microscopic that Mr. Woolsey would actually put a risque element like a transvestite into one of the games that he had to censor so much of that kind of thing out of.