I don't personally have any issue with the last chapter's end. It was a little weird because transitioning is a very big decision, but both were choices he made for his happiness. He said that the reason he wanted to be a girl is because being a guy got in the way, i'm thinking that he might've meant dating considering he chose Kaouru over transitioning. Like, maybe he was having trouble finding men who reciprocate? From my personal experience, i can relate in that i've thought many times that things would be easier if i was a female because the guys i'm attracted to tend to be straight... Like every crush i've ever had was straight. The obviously gay guys tend to be flamboyant and just not my type. I fall for the manly dudes and find out they're straight and it sucks. I've never wanted to transition, because i love everything about the male body, but i can see how someone else would in this position. Then he finally finds, not just someone he's interested in, but someone he has a full blown crush on who wants him as a man.
Don't be a hypocrite by condemning a poor representation of gender issues, when you use terms like uke and seme and overlook the homophobia in yaoi. You say it's problematic that it seems like the character chooses to be male or female, rather than it being an inherent trait, yet nearly ever bloody yaoi has characters saying they aren't one of those gays, they just fell in love with one man so identify as straight. And use heteronormative steretypes, to the extent where charcters are criticised for being "chicks with dicks". Then you have the sexism not only within this uke/seme thing but how actual women in yaio are represented. So why only stand up for the "T' in LGBT, but ignore the problems within yaoi that you read concerning the "LGB"?