Eh, as much as I'd like that to be true, I think you underestimate people ability to get into conflict over insignificant differences.
Moreover, not every transwoman wants her genital anatomy altered. There's plenty of other differences in how transwomen transition. Magic would only add greater ease and precision in that.
Trans women and cis women are both women, even IRL, but even in a magic universe, there still would be differences in flavour.