Considering that you started your comment off with an acknowledgement to respect the author's choices, your following words don't really honor that. When asked about the lack of trans options in the game (which is a valid question) the author didn't say that they didn't want to include them They didn't say that they believed they shouldn't be included. They said that they didn't feel they could write those options faithfully or realistically, which, to me, feels a lot more inclusive and respectful than a clumsy or misinformed attempt at simply having token representation.
The author focuses on the diversity they can write, because readers deserve to see a truthful and sincere exploration of these ideas. In their first response to you, they even mentioned feeling more confident in writing trans perspectives and that they were including that in their next work. This shows a commitment to genuine inclusion. This shows growth. But you ignore that to continue harping on what you found lacking in the story.
The author also doesn't address ageism, or ableism, or neurodivergence, or religion, or a plethora of other identity issues. But that may not be what the author is attempting to explore, or is even capable of exploring in a way that feels sincere and well-informed. This is also not a salad bar of a story. We don't get to order off a menu for what we think the author should be writing about.
Isn't it more important to celebrate the inclusion we do see, and to acknowledge the author's intent to include even more, to continue growing, to offer more and more genuine, respectful representation, than to sit here and wag a finger at them for not writing the exact story we want to read?
Just a reminder that this IF is clearly a labor of love. Keyword: labor. A lot of time and effort out of someone's life. And it's on here for free for us to enjoy and engage with. Or to not engage with. Your choice. But if your motive for your comments was to argue for the inclusion of something in another person's creation, I have to tell you that this is not the way to go about it. It doesn't read as helpful. It reads as entitled and demanding, even if it started with good intentions.
As a writer myself, I can also tell you that the best way to see the representation you want in stories is to write your own. It feels trite, but it's true. Just a thought.