It's not ambiguous though. The only thing ambiguous is whether or not the author is sincere about the very blatant and undeniable transness of the protagonist. Well, that and the transphobic readers who wish to deny trans existence who twist themselves into knots to try to explain why this character couldn't possibly be trans.
If that's where the author goes, then that's what is being presented.
That's my whole stance.
I'm not here to deny the reality of transfolk, in reality or in fiction. I'd just prefer to not put words in the author's mouth and let them speak through the story.
But I do try to let the author dictate the story they wish to tell, and not put my own interpretations on their narrative, however justified I may feel they are, until they're backed in no uncertain terms by the individual who is actually putting pen to paper.
And at present, there's an argument that the reason the protagonist is stressed over discovering they possess a penis is because of what canonically happens to men found on-campus within the story of the game the protagonist is currently existing within - and not explicitly because of dysphoria.
Would it be great if this was a trans protagonist realizing their dreams by being Isekai'd into the setting of their favorite escapist fantasy from their old life? Abso-fucking-lutely, I'd be overjoyed to see something like that represented in contemporary manga in a way that's unequivocal in its presentation.
And sure, it could be
interpreted that way, and I'd argue convincingly so, but I'd prefer to not make that final call for the protagonist or the artist until it's stated as such by them - because it's really not my place to do so, even for a fictional character.