I.... think you need to read a wider range of manga on LGBTQ+ themes and research more into this stuff before making a bunch of claims like this?
Like... have you read things like "X-Gender", a manga about the struggles of a nonbinary person in Japan? Or "My Lesbian Experience with Loneliness"? Like, manga by LGBTQ+ people about the real problems with how Japanese society kind of tries to sweep nonconformism under the rug and then be all like "We're Japan! We don't do that here!"
You can't just read a yuri series about cute schoolgirls having a chaste little heartwarming relationship between two femme-presenting teenage cis girls and say "That's what ALL LGBTQ+ media should be like!" just because you're more comfortable with depictions of queer identities and relationships that don't show the harder side of how society treats anyone who doesn't conform to established social and gender norms, or present relationships that might make you really think and reframe how you think about gender and sexuality.
I have a degree in Japanese, and people would ask for years "why didn't you go to live and work in Japan?" and it's precisely because of that thing of "We all agree to do things like this!" that outsiders who don't know the country well take to mean that everyone happily conforms, when it's actually more like nonconformity is stamped out, not violently, but simply by being made very difficult. Homosexuality is mostly tolerated in Japan so long as it stays in "allowed places", so schoolgirl romances = okay, but like bleaching your hair, it stops being okay as soon as you leave university, when you're expected to conform with black hair and getting married into a heterosexual relationship. Cross-dressing is allowed if it's at a cross-dressing bar or Takarazuka performance, but just being trans isn't tolerated. Trans people have to get themselves certified mentally ill and then sterilised!!! That's not okay!
There are people who protest this, but they just don't have the same about of social power as the LGBTQ+ movement has managed to gain in some other countries, because it's so hard to get into a position to have your voice heard in Japan while being nonconformist.
There's a good overview of how bad it is, and on the actual ongoing debate around it here: