I just wanted to let you know this is not proper viewership etiquette. It's one thing to question a part of the story and make a suggestion, it's another thing to ask the author to rework multiple parts of their story, even if it's just small changes, to fit your needs.
I can understand wanting there to be more inclusion for viewership and having a trans option for the MC is a valid concern. But the author has clearly stated that they didn't feel like they could write it in a realistic way, especially considering this is their first IF.
This work focuses on self-discovery, the importance of words, and growing outside of what the society tells you is acceptable. I believe that's puts even more importance that if the author decided to place in a trans option for the MC, it should be clear and explicit and properly shed light on the struggles a trans person has when first questioning their identity. It shouldn't be vague remarks here and there that have nothing to do with the story.
As Orangeflavor has pointed out, there are many other aspects of identity that isn't addressed in the story. Are you saying that the author should make vague remarks about them too? They should edit their story to include ambiguous suggestions to those identities that would only work to confuse the reader of who they're actually playing? As you've said, these identities and the role of gender have absolutely nothing to do with the main story line, so why the hell would the author put in any notes of them if they're not going to mentioned again later on? It's a very ignorant ask of any viewer to want the author to make changes to several parts of their story. Especially with an IF, where the author has to write and code it out properly.
This story was one made out of love and something the author was very clearly excited to show the world. I'd much rather the author write the story as they have and be happy with it, rather than the author makes several small ambiguous changes to the writing and be unhappy and uncomfortable with giving an important journey a flawed execution.
Instead of dragging this whole thing out with your multi-paragraphed "advice," the proper response to this entire thing would've been to address your critique to author, possibly make a short suggestion of what could've been done, and if the author said they couldn't do that for whatever reason, then you thank them for responding and move on. If you cannot enjoy a story without a certain detail being included, then just don't read the story. Read another that's already fitted to your preference, don't make the author feel bad about not including a detail they felt they couldn't realistically write and then tell them how they should write their story.