Kanojo ni Naritai.is a bit different, because it all happens in a single school, but actually, I'm not interested in stories about LGBT communities.
While I understand the need for some people to group up for protection, the whole concept of "communities", whatever group they are (black, white, gay, latino, christian, jewish, muslim, abc, trans, all of the above, whatever...) looks like a failure to me. Even the flags irk me. It reeks of nationalism. And nationalism is war.
I know that the model of the American/English society is built on communities, but it looks like apartheid to me. It's a model built on distrust. It looks comfortable, at first, because you're among people who share your worldview, but these communities are doomed to oppose each other because isolation leads to groupthink and incomprehension. As intelligent beings and part of he same species, we should be able to live and let live together, whatever the background, identity, or sexual preference. We should have grown out of the tribe mentality.
Now, I sound idealistic and in contradiction with my previous rant about how these manga are angelic, but what I have a problem with is the concept of "people of the same feather flock together" and how it somehow is something positive in the long run and it solves problems. These people help each other, but at the same time, they isolate themselves from the "other". This, in return, leads to hostility from narrow minded people from all sides who feel threatened by the "alien" community. We have seen here numerous times that some LGBTQ+ people can be as intolerant as anyone when it comes to other lifestyles, especially when they feel secure in their group. Lesbians hating on trans, trans hating on cis, gay hating on bi, etc...
I don't have a magical solution to these problems, but I'm sure as hell that communitarianism isn't one.
It's silly to cry about the sky being blue. You better start getting used to it. Humans group up with other like minded humans. It is our nature.