I'm moderately familiar with Japan's breadth of historical positive depictions of varied sexuality and gender, and I've read a bit about what it's doing on that front at the present. I've also read about the opposite, so I know it's not perfect either. "Hella homophobic" may have been a bad way to phrase it, but I won't say it doesn't turn that way too often for my tastes.
I doubt you're "modestly familiar" as much of that work simply only exists in Japanese. But it's taught in the classroom. And a "bit" of research, while surely better than none, still isn't enough to justify your commentary - what right do you have to make uninformed statements about a civil rights movement in another culture? The reality is, there are problems in specific areas of course, but there are a ton of areas where it genuinely excels and you REALLY can't erase those (or pay them lip service as you did above) without devolving into an overly simplistic "me more civilised/them less civilised" rhetoric. I know several people who moved to Japan (from America and the U.K.) specifically because they felt safer and less discriminated against as an LGBT person there (PARTICULARLY a trans friend of mine). Under your understanding of Japan this would appear inconceivable. And yet it happens - a lot, actually.
You don't speak Japanese, you haven't been to the country, etc. Judging Japan largely based on sensationalistic news reporting (ask yourself: which stories get reported in English vs which don't), comic books, and cartoons largely aimed towards teens would be like judging America based on tabloids, Spongebob, and the Sunday Funnies.
Surely you respect the culture enough to know your picture is woefully incomplete, extensively source-biased, and couched in a fundamental lack of understanding of your topic (based on a "bit" of research, entirely in Western reporting). Just being a generally progressive person doesn't give you carte blanche to say ignorant, misinformed, or problematic things about an entire culture. Either frame your statement as a question "isn't it the case that...." and accept corrections or do the proper research so you can speak in an informed manner. Otherwise you can't help but essentialise and simplify an entire culture as your understanding of it is essentialised and simple. And I shouldn't need to tell you how troubling that is.