As a honest, non-trolling comment, I think I would take a fairly "conservative" stance on the issue. That being said, normally I don't align myself as a conservative but rather a liberal. And because I am a liberal, this topic, IMHO, is far too foreign for me.
I felt quite uncomfortable while reading this manga - I believe that this is actually a plus point, since it means that I can feel the suffering of the characters, and certainly the mangaka nailed it.
Despite such discomfort, I reread it, not once but until fourth times trying to understand the situation, of what both protagonists are, what their problems are, etc. However, I became quite confused the more I read it; at one point, I was like, heck, who is who again? The concept of trying to find one's own identity is too foreign for me. Probably I am a "cishetero" guy so this matter never comes to me. But honestly, I don't see it as a serious struggle, since I don't care much about what people around me want to become, nor what people think about me (the society where I live in is also very traditionalist as well, but heck, screw that). You guys do whatever you want, I do my own stuffs, as long as it is not a bother to the others. I believe, IMHO, "flaunting" your "identity" is quite a bother to the others, actually. If people are interested, you can try to explain to them, else it creates needless arguments with both sides, for a certainty, never try to understand the other. This is why despite being a liberal I try to distance myself from the current progressive trends. It is too indoctrinate-ive for me.
Because of such foreignness, I actually can somewhat understand Miki. She is foreign to these matters as well. What Yuuko "explained" to Miki became "preaching" - as Miki said, their attitude was bad. You don't simply try to "preach" it to uninterested people. SInce the first impression was like that, adding the fact that Yuuko was Miki's rival, it became quite natural for Miki to be such an ass.
Anyhow, what put me off the most is, why would Miki liked Makoto? I see little reasons for Miki to like Makoto unless Miki herself is a lesbian/bisexual and comfortable with a transgender. If she is comfortable with a transgender, it is illogical for her to show that much ignorance, like me, on the matter.