I kind of understand the author's intention. "yougogirl" took the words right out of my mouth and explained the issue with this manga very well!
This story reminds me of a story about a trans male character that I wrote when I was a kid. I thought I was writing a such a deep story, but in reality I was just info dumping.
This manga has a lot of potential, but the author didn't fully exploit it. I'll admit, I can be biased and easily triggered by people who don't understand me, because I'm tired of having the same conversation over and over again. I understand the feelings of our main characters. Unfortunately, this author has pushed their subjective viewpoint into the story, which isn't good from a writing perspective...
The author need to see things OBJECTIVELY. They had to do that if they really wanted people to understand the main characters. The concepts of nonbinary, agender, bigender are inherently difficult for outsiders to wrap their heads around. Making Miki the antagonist instead of a character representing "outsiders" is A HUGE MISTAKE.
Nobody likes being treated like they're ignorant. When you insult someone, even if you're in the right, they'll refuse to listen because of their own ego. (Want to see examples? Check out this comment section!)
Perhaps after gaining more experience, they will get better with their works. Honestly, I appreciate the effort to spread awareness.