You seem a little unclear on the meaning of the word "essence." Subtexts and stories whose themes are ambiguous or which can be read in multiple ways are the opposite of "essentially" trans stories.
By this argument, the Matrix isn't a trans story, which is extremely untrue, as confirmed by the creators. Y'know, two trans women
I haven't really read up on the current conversation mind, I have no thoughts on that. But queer themes don't need to be, and are very often NOT, explicit. Especially considering how people treat trans people. I dunno if I personally would call this a trans story but I see nothing wrong with someone taking it that way, right?
Anyway, the actual story. I like that she still calls her "her crush"~ that makes me happy.