I think the question has been taken slightly the wrong way. Having more non-binary and/or trans characters doesn't necessarily mean that they'd want to add characters to the game; it could also be taken as "I feel like it would have been nice if the characters from the existing cast had been more diverse".
And in that sense, I think OP's wish is completely valid and understandable. While I personally don't mind gender presentation among the cast the way it is now, I can see how someone would feel that it'd be nice to have more representation.
However, I do think that with respect to how long the game's been in the works, and that Ame originally started out not wanting to change things about the characters from her league, it's also not something I'd see as a flaw.
I feel that if Reborn was a new game that Ame had only just started working on, we would probably be seeing quite a bit more diversity among the cast. She certainly isn't the type of person who would shy away from doing such a thing.
But Reborn isn't that new, and many of the characters have existed this way for years. I remember the topic of changing things around came up in the E16 discussion thread in relation to the storyline, and Ame said that by the time she decided that she doesn't want to restrict herself by sticking to "league canon" any more, a big part of the game's story had already been planned out and set in motion. So changing the characters this far into development probably wouldn't have worked well.
Creating diversity is, to a good extent, a learned skill for writers. And sometimes, especially when you're working on an ongoing project of which parts have already been published, it's not possible to just go back and change things around. And it's too late at this point to introduce a completely new character arc about it.
So you just acknowledge it and move on, and do it differently next time.
That all said, there's nothing wrong from having your own headcanons about the characters' gender identities. Like Commander said, a good character is not defined by any single trait. You could switch the gender for most if not all of the characters and the story could still happen just the way it did.
Sure, it's not the "real deal", but if you think about it... most characters in the game have never given clear stances on their identities. Imagine what you wish. I've been headcanoning Fern as a trans boy for ages now.