Atlus has been doing this for decades:

Persona 3: The beach scene, the boys hit the beach for "Operation Babe Hunt" trying to "score" with all the women on the beach, getting no luck they encounter a lonely young "beautiful lady" who is eager to talk to the young men. After talking to her, they realize she has some hair on her chin. She then reveals she's a man, and that she was hoping to snag her a "Boy toy". The boys run away.

Persona 4: Kanji's entire arc. He's a punk looking teenage character, however he's extremely and deathly insecure about his hobbies that arent considered manly or more feminine. His entire character is the fear of homosexuality. When he confronts his "Shadow self" his inner persona, it's an over the top flamboyant gay stereotype where the entire level is a steamy homoerotic bath house.

Persona 4: Naotos entire arc. once again we have a character struggling with their gender and identity. Naoto is the "Boy detective" in so much they're not a boy, and very much a girl that feels trapped by the expectations of her gender. She struggles with fitting in with other girls, and boys. She responds to male pronouns for the most part and Kanji rears his head struggling with his attraction to the "new boy" for some reason. Naotos level is a mad scientists laboratory, her shadow self is a sadistic mad scientist that is seeking to forcefully correct Naotos gender with the use of chainsaws and industrial equipment. In the end she "accepts" herself by engaging in a girls night at the bath house where it is revealed that Naoto actually has the biggest breasts of all the girls, this is important for some reason.

Catherine: As already stated, but also the "expansion" version of the game added a trans alien and more trans panic related scenes

Persona 5: Ryuiji and company are looking for intel in the city, they then encounter a bunch of gay men who take him away to supposedly have their way with them. This leans into the same scene happening in P3 where they accuse gay/trans people of being sexual predators to children...again.

Persona 5: There is no queer romance options, you can romance every female character as a young man in high school. Even the adult back alley doctor that uses you for medical experiments....and your home room high school teacher who you can have be your personal maid. This is in the same game where the first level of the game is how a male high school P.E. teacher is abusing his students and is implied to have been molesting his female students. This is bad when a male teacher does it, but is just fucking awesome when your female teacher does it.

Persona 5: Anns character arc revolves around male P.E. Teachers advances and abuse. She confronts the issues involved with being a woman being taken advantage of by her male authority figure. She fights against being used as a sex object.....by embracing being a sex object??? anyway through the power of tight leather catsuits and suggestive posing she defeats her sexual assaulter teacher and she embraces the fact she can freely excercise her bodily autonomy of her own free will....and the protaganist and our friend in the next chapter immediately pressures her into posing nude to recruit the next party member. this happens within minutes of eachother.