that has less to do with japan and more to do with the fact that niche music doesn’t attract laypeople. you can find the same kinds of shows all over the united states for example
For the local music scene in my city (Kitchener ON), if you want a quiet, respectful, focused environment in which to enjoy, skip the pub sets and go to the house shows instead. Almost all the local artists play them, and there are a lot that are pseudo-public. Like, they're not advertised openly, so you need to ask the artist to find out, but you also don't necessarily need to know the hosts— it's very much a friends-of-friends type affair, and in my experience very welcoming.
I think Japan might actually be different in regards to music performances. I know folks from a few lesser-known punk bands, the kind that might get 50 or so folks at a typical club show on a good night in the US, that did tours in Japan. They described the same kind of reverence at their shows in Japan, and punk isn't exactly known for reverent crowds. This was 10 to 15 years back, so things may be different now?
If it was just because of the genre, their brother would notice that anecdote everywhere and not just Japan. The drummer in my current band plays with several groups (very common for a skilled drummer in NYC), and he just got back from a 2 week tour in Japan and had the exact same things to say. Crowds were way more respectful and focused on the music.
I agree though that in general niche music is more respectful than more mainstream music, at least in the USA. Harsh noise and stoner sludge/doom shows have had the most polite people in the mosh pits in my experience.