The manga: a college guy meets his childhood friend, who was formerly a boy but is now a woman, and has run away from home after an unspecified disagreement with her family which has left her with a significant amount of trauma; it's implied she was bullied heavily in the time since they've last seen each other.

But don't worry, she's not trans! She just got an illness which turned her into a woman!

The manga: a high school boy with an interest in make-up uses his gloomy, depressed (male) childhood friend as a model to improve his skills. This causes said friend to have an "awakening" and start dressing as a woman, and to overall be a much happier, brighter, outgoing person.

But don't worry, the friend is not trans! He's just a boy who crossdresses because his childhood friend likes him better that way!

The manga: a high school boy joins a club where the members can turn into magical girls, which in his case involves physically transforming into a girl. When in girlmode, he's much happier and enjoys his life much more, and overall prefers staying in girl mode; when the ability to transform is temporarily taken away from him, he sinks into a deep depressive episode.

But don't worry, he's not trans! He's just a boy who enjoys being a girl!

The manga: a college student loses a bet and has to crossdress for a night out on the town, and meets and hooks up with a butch girl; they fall in love and start dating. The boy always crossdressed when they meet, and starts enjoying being "treated like a girl" in the relationship and starts crossdressing even when he doesn't have to meet his girlfriend and enjoys activities such as clothes shopping and make-up and putting on nail polish.

But don't worry, he's not trans! He's just a boy who crossdresses to please his butch girlfriend!

The manga: a guy is magically turned into a girl as a result of saving his best friend, the crown prince, from an assassination attempt. The prince decides that he has to take responsibility, and asks the new girl to marry him; despite being smitten she refuses, wanting to date first. She is later offered a way to go back to being a man, but when she does turn back she's disgusted by her own appearance and depressed all the time, ultimately deciding to stay a girl.

But don't worry, she's not trans! She's just a boy who's been magically turned into a woman! And decides not to turn back when she can! Because she's not trans! Somehow!

"But we can't write trans women in manga! It's just not something that you do!"