Not to pick on your post specifically, as I'm really addressing several here, but... there are LGBT people in Japan just like anywhere else. It's a little silly to frame it as if it'd be impossible for a game coming out of Japan to handle these things well, y'know?
So I feel like going "well, it's Japan..." is still excusing - or at least, tempering criticism - too much even for things like this. There are certainly people/organizations they could consult even if they have no one (that's out) on staff. And though obviously representation among the developers as well is the ideal goal, it is obviously still possible for there to be media - and Japanese media - that handles this well due to research and care. Totally understandable to think "I don't want them to try if they're just going to make it worse", of course, but still.
The thing here is that the "overarching story" doesn't necessarily need to be where this kind of thing would mainly appear? Because - though I have not reached them myself - that's not where the straight relationships play out.
At least where I am now, maybe 1/3 through the game, most of what you learn about characters is in Support scenes; I know in the back half characters will fight each other, so there'll be some more in the main story, but Supports are still probably gonna be where any bonding/romantic implications happen. These are distinct scenes between two characters, which can be gated by story progress but are only unlocked by increasing a hidden (at least numerically, you just see when it increases) stat through them aiding each other in battle or some of the various activities you can do at the monastery. These aren't inherently romantic; the main character has Supports with every character, and everyone else has their entire house + a few others. If a character has Supports available with another character, they'll at least have scenes for ranks C and B. Some have A rank as well, and only the main character can get the romantic S ranks (which are apparently not actually romantic for the m/m pairings described in the article). There's some more stuff to it (some pairs have 2 scenes for a rank), but basically these scenes are entirely optional and separate from the main story.
Since these Support scenes are where the real meat of the direct interactions between characters happen, there'd kinda be more or less no additional focus on learning these things or exploring relationships compared to straight characters/pairings. The only thing is that I believe that except for the main characters, the game doesn't even show anything explicitly romantic for pairings till the ending due to them not having S ranks. But even then, that wouldn't be an obstacle for showing this through Supports if the character was only gay, or otherwise if they were acknowledged as being bi even when not in a same gender pairing. In my opinion the game actually provides a good structure for exploring this stuff, but... it doesn't.