Thanks for the thread OP. Good to get the major points outlined in one place. Full Body is very, VERY bad, but even if you could explain away its bullshit as being an innocent mistake, there's definitely a pattern here.
I wanna give a shout out to a few things not mentioned in the OP. In Persona 4 Dancing all night, which he didn't direct, but he did produce according to wikipedia, there's this gay dance instructor who pretty much fulfills every gay stereotype in the book? He flirts with everyone, he's very camp, his design is super duper colourful, he's... well he's a dance instructor. He's honestly not that harmful compared to some of the stuff mentioned here (At least he seems to be liked by the main cast despite a fair bit of othering going on), but if we're talking about trends then I figure this is worth mentioning.
Also, Lala-chan in Persona 5. I know a lot of people like her. *I* like her. But with the trend established, I'm gonna call Persona 5 out here. In any other game I wouldn't read into this so much, but I ran out of trust ages ago, so here we go. There's a scene in Makoto's social link where she and the protagonist visit her bar. I forget the details, they're not important, but they get into a conversation where Lala-chan talks about her time as a little girl. Makoto's reaction to this is just... shock.
This isn't talked about afterwards.
There isn't a follow up line that establishes that Makoto is very sheltered, and thus she reacted inappropriately.
This is a punchline. A bad one.
It's my belief that Lala-chan only ended up largely pretty ok, because she doesn't get enough screentime. Because imo, the cracks are showing already.
(Also, Kanji is my boy, IN MY HEART HE'S BI, but realistically he's not in actuality. It's pretty queer baity tbh.)