... What if Koopas usually reproduce like Namekians do?
Given that Namekians are biologically female by standard definitions (they just socially present as male), that would make the Bowsette thing make significantly more sense - it's a species change, not a gender change, and with the commonality of powerups EVERYBODY there is used to species changes
Although you'd think losing the ability to present as male would be more offputting still
She isn't. During Sunshine, Bowser Jr. kidnaps Peach, claiming she's his mother, but at the end, Bowser has a talk with him saying that it had been a lie when he said Peach was his mother. (And Bowser Jr. says he'd already suspected as much.)
No clue is given on who the mother is, though.
The closest thing we've ever gotten is a joke fanwork webcomic from back in the 90s with a "Clawdia Koopa" that's basically Bowser in a wig and pink dress.