I think that's a big part of the reason why Yuuko got angry at Makoto. Makoto has their struggle, and their coming out is (literally) on the public stage, but where does that leave someone who isn't obviously genderqueer? Being non-binary when it doesn't entail looking like a boy in a skirt can leave you feeling invisible.
Add to that the weight of gendered expectations for girls. It's bad enough if you don't conform to those expectations, but if you don't even identify with the category of "girl" it's much worse. Like putting on a double act. Yuuko doesn't want to be seen as a straight girl who's dating a boy, or even a bi girl, but that's how society sees her relationship to Makoto.
Social dysphoria is difficult to define. I'm DMAB, but more agender; I bristle at being called gendered names, or being sorted into a group of my assigned sex at birth. I relate a lot to Yuuko. You're right, I don't face the level of overt discrimination that a binary trans person would, but that doesn't mean there aren't social difficulties involved in it. For instance, there isn't really a name for my sexual orientation; I like girls (cis or trans) and DFAB non-binary people, but I'm not bi or pan. But "straight" doesn't work, because I'm not a guy. When I do act more gender nonconforming, I'm usually taken for a gay femboy, but I feel like a complete outsider in gay culture.
When I don't have to present as a guy or binary girl, I'm much more relaxed and open about myself. IME, asexual people are really good about understanding gender nuances, and I'm gray-ace so I can fit into that culture.