... 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