Imagine a writer who wants to write a character who is sick. They do their homework, research symptoms, find a treatment that's supposed to work sometimes, etc, and they write their book. Later, it turns out Science Has Marched On, and what the writer thought was a single disease was actually two different ones with overlapping but non-identical sets of symptoms. The things people thought were multiple unreliable treatments for a single condition are actually fairly reliable, just that some work on one disease and other work on the other one.

Our writer, it turns out, has written their character with symptoms that are actually a lot more likely given Disease A, but recovering after being administered the treatment for Disease B. This is not logically impossible or anything, some of the symptoms could have had an unrelated source, or the treatment had failed and recovery happened for other reasons, but it is still an improbable situation. Suppose the future fandom of this work has lively arguments about whether this character 'really' had one disease or ther other, arguing about the various improbabilities of each case.

The correct answer, of course, is 'neither'. The author's world-model was flawed and the writing derived from incorrect assumptions; there is no real version of the character who must have one microbe or another in their blood, and so while one might certainly headcanon one or ther other there is no meaningful sense in which one can talk about which disease was the 'real'.

I have no idea if this situation has ever happened exactly like this; it seems likely something like similar has, given the evolution of medical knowledge over time, but I have no specific examples in mind. No, this is all a metaphor about the TV Tropes page on Ambiguous Gender Identity.

"Is this character really gender non-conforming, gay, or trans?", whenever there is any actual ambiguity on the matter, should be assumed to be an incoherent question unless the author is themself queer(and even then that doesn't guarantee anything, but it improves their odds)

If I never read 'ah, but in the end she said she never really wanted to be a boy, she was just uncomfortable with her role as a woman in a sexist society, so she was not a trans man after all' as an argument again it'll be too soon.

(a different but related case being 'well, literally everything on the page points to her being a trans woman but the author uses male pronouns for her in WoG', which is not a question of ambiguity but of the character being transgender and the author being a transphobe)