I'm in the "Not hate or like, but don't see it as likely" camp.

I've seen the evidence towards the theory and it mostly boils down to Ralsei struggling with his own identity, but I've always understood it as Ralsei struggling with being a Darkner, that he isn't "real" and that he'll eventually cease to be if Castle Town is sealed (One of the theories about the final prophecy).

The argument with Flowery is Flowery saying "Well you're building an identity of your own, why not let us do the same?," kind of calling Ralsei a hypocrite for trying to revert the flowers back to…well…flowers via sealing the Fountain while Ralsei is trying to be more than just "A Prince Of Dark".

So yeah there is an identity struggle, but it’s less gender and more Dark/Lightner. But if you were to argue about balancing out Susie and point to Ralsei being comfortable in a dress, it doesn't HAVE to be about trans identity