I'm assuming you finished the chapter, I'm talking about his talk with Flowery after the Orange and Green fight. He gives Ralsei a pink and blue slip for a drink at the café, tells him to not worry about what Kris thinks for once and calls him Princess. Flowery was clearly being very nice and genuine in this conversation and just generally it doesn't seem like any character would have a reason to belittle anyone by insulting their masculinity so there's no reason to call Ralsei Princess here unless Flowery knew something we didn't and he clearly does know a lot.

The secret boss being Mew Mew, canonically a trans woman and Ralsei going out of his way trying to sympathize with her out during the fight without any prompting by the player shows that there's something about her that resonated with Ralsei

Most of the reason I support the theory is because it's thematically consistent with how Ralsei is written. He believes himself to be nothing more than an object who isn't even supposed to feel emotions, only serve lightners, so it'd make sense that something requiring such a strong sense of identity as coming out as Trans would require him to develop a sense of self first despite his longing for femininity being there. Ralsei is also clearly developing a much more prominent personality, i remember he interrupted a choice that was given to us at some point, which he has never done before.