After viewing the comments section of Kiyohara, it was pretty ugly. Yes, there were ACTUAL hateful transphobes in the comments, but also unreasonable people who accused others of being transphobes for simply sharing different views, and also people who did not even care about the argument, but rather tried to fuel the fire as online trolls do.
I have family in Japan and personally know a few crossdressers; most of the arguments stem from what I feel are people forcing their beliefs on another culture, both in the context of Japan vs Western culture, and Trans vs Crossdressing culture.
Kiyohara is referred to as what is known an Otokotonoko. Even non-crossdressing men can be referred to this as it is mainly referring to a man's feminine gender expression. I think this is where our understanding gets lost in translation. You can be an Otokotonoko and still identify as male and dress like a man if you happen to look feminine or embrace a feministic side to your personality.
It is indeed a fact that the term is more often commonly associated with crossdressers. But to say all male cross-dressers are trans-female is wrong and disrespectful. It is like calling all drag-queens trans-females. Yes, some drag-queens do identify as female, but others of that resilient and diverse community have different reasons for crossdressing outside of gender identity.
Japanese crossdressers are no different. Some crossdress as a form of self expression, others as a fetish, but a majority do it simply as a hobby or fashion statement. One otokonoko I regularly met on a daily basis dressed as such because HE (emphasis on he as he still identified as male) wanted to feel liberated from societal norms. Another did so because SHE felt it is closer to their authentic inner selves. Crossdressing is not always about gender identity. It can be, but to automatically assume it is isn't a Japanese thing, more of a Western thing at this time.
In Japan, crossdressing is way more accepted than actually identifying as trans. I wouldn't be surprised if people were using crossdressing as a guise to embrace their true selves, but at the current time, a male crossdresser is expected to still identify as male.
In Kiyohara's case, people were arguing that they saw "MTF" being used to refer to Kiyohara in the official translations which proved Kiyohara identifies as a female. The author, however, stated Kiyohara is a male. I'm inclined to believe the author's intention was to portray Kiyohara as the type of otokonoko who embraces his feminine side.
There was a line where Kiyohara flat out states wish they were a girl but again, I think this is a situation lost in both language and cultural translation. Japanese language has a tendency to not be direct in its meaning.
A lot of the nuance and meaning is lost during translation because Japanese does not operate like English and vice versa. For example, in Japan, when you ask a person "O genkii desu ka?" as in "are you doing well?", one accepted reply is "okagesama de". It literally means "thanks to you"
"Are you doing well?"
"Thanks to you!"
That makes no sense in English because the person asking typically had no responsibility in our mood/liveliness, but it carries a whole slew of meaning in Japanese that makes it equivalent to "I'm doing fine/great!"
Consequently, Kiyohara's simple statement, "I wish I had been a girl", carries a more complicated connotation of "if I was reborn again, I wish I would be a girl but accept that I have currently been born a male" type of meaning rather than if a person said they wish they had been a girl in English, they quite literally and directly mean they wish they had been born a girl in their current life with no other complicated nuances or roundabout meanings surrounding the English statement.
In all honesty to this whole argument though? I could care less what Kiyohara identified as. Kiyohara was a compelling character who was written intricately and with great care nonetheless and their gender identity did not detract from the story. STFU and just enjoy it like the author intended.