He didn't magically turn into a female y'know.
The relationship would still be classified as yaoi or shounen ai since both members are of the male sex.
The main reason he wants to be born a girl is because his crush doesn't at first appear to be interested in males, but it seems like he leans more into bisexuality from the conclusion of this story. He doesn't want to be a girl due to personal conflicts, but for someone else.
Also I knew someone would eventually say something like this, every time we got a character even mentioning wanting to be a girl in passing we got gender studies experts chiming in immediately assuming trans. When the situation requires more nuance. It's more complicated than that...
It's hilarious how you talk about things like gender and sex while conflating the two, and then talk about the situation being complicated and requiring more nuance, while at the same time showing a complete lack of understanding of the complexity and nuance of the situation.
Just to start with, your sex (what genitals and DNA you were born with), is not the same as your gender (whether you express yourself as masculine or feminine to yourself and others). Maybe do some research learning the most basic of basics when it comes to the discussion, before chiming in like you know anything at all about it.
Also, I thought I was pretty clear that it's definitely still very open-ended as to if they did anything like transitioning, or are just expressing themselves as a feminine gendered person but staying their assigned sex of male. Also, we don't know anything about the potentially many reasons they want to be a girl. They COULD be just doing it for this one partner (which is kinda sad), or they could be interested in this one partner as part of WHY they want to be a girl. Plenty of gay men get turned down because someone they are interested in doesn't like men, and only very few of them then go out and disappear for 6 months and come back presenting their gender as female. That doesn't mean they want or need to transition, but that also doesn't mean they didn't, and we don't know which is the case for this story.
My whole comment was if they DID (which again we don't know!), then it would no longer qualify as BL, because they would be by all accounts a girl, except for bigoted people like you that would probably try to still tell them that no matter what they are a man, like it's any of your decision/business.