First, are you going to provide some sort of source for that claim? Chapter number, page number, etc...?
Second, yeah, actually, the story can work perfectly fine if Kitano is trans! Really easily, in fact; we've literally already seen the mechanism for it to do so: Girly acknowledging that he didn't understand what Kitano was going through and changing how he looked at her literally just happened on-screen. The author could very easily make "there's only one [cis] girl" a massive red herring by simply having Girly acknowledge the others in the class as viable targets of his affection, just like Kitano. That basic idea isn't even new, it's literally how Stop!! Hibari-kun! from the 1980s worked with Kosaku having to let himself see Hibari as a woman and therefore making his attraction to her acceptable.
First, are you going to provide some sort of source for that claim? Chapter number, page number, etc...?
Second, yeah, actually, the story can work perfectly fine if Kitano is trans! Really easily, in fact; we've literally already seen the mechanism for it to do so: Girly acknowledging that he didn't understand what Kitano was going through and changing how he looked at her literally just happened on-screen. The author could very easily make "there's only one [cis] girl" a massive red herring by simply having Girly acknowledge the others in the class as viable targets of his affection, just like Kitano. That basic idea isn't even new, it's literally how Stop!! Hibari-kun! from the 1980s worked with Kosaku having to let himself see Hibari as a woman and therefore making his attraction to her acceptable.
In the literal next chapter, chapter 3, Kitano and the others acknowledge themselves as boys, this keeps happening throughout the whole story, it's one of the main sources of drama, conflict and reflection of the narrative.
First: By Eguchi own words in the manga and his personal social media profile, Hibari is a boy. His relationship with Kosaku is an homosexual one, and that's what makes it so charming and daring.
Second: No, the story wouldn't work because this would make Kitano a girl, and break the idea of a classroom of crossdresser where a single girl exists. Kitano being a girl would reshape the work in a way that would take away the original charm of the narrative.
The love Kitano has for Girly is already viable, he doesn't need to be a girl for his love to take form or reach Girly.
We see the foundation for this on chapter 2, Girly couldn't understand why Kitano would want to be girly, but he could sympathize with it, in the same way he can come to understand Kitano's homosexual feelings.
Honestly it's even weird to bring up viability and acceptability as justifications to why Kitano should become a girl. Shonen magazines have changed a lot in the last years, you know can find explicit boys love and homoerotic romance in it, this is something that has been happening since the time of Hibari-kun.
This is an Otokonoko manga, it was sold as a boy-meets-boy story in Japan. It would be weird and unfitting if all of sudden this story made one of their main crossdresser become a female character. You lose the homoeroticism, the crossdressing, the idea of a boy expressing themselves in an unconventional way, you handwaved the struggle and conflict that the work tries to build with Kitano's homosexuality and non conventional expression and how this affects Girly, his view of self, gender, relationships and Kitano.
I'm not opposed to the idea of Kitano being trans in headcanons, but in canon, in my view, him being a boy is what makes the character and manga shine.