It's not common, but it's a notable widely publicized issue - so if you're writing a video game and you want a low-level antagonist for the hero to fight, it'd be one of the default options.

It’s common enough that there are women-only cars on the subway in Tokyo.

Germany has also tried women-only cars and there have been discussions of having them in the UK, but they were rejected not because they're not needed but due to the optics https://en.wikipedia.org/wiki/Women-only_passenger_car#Europ...

Not saying this as whataboutism or to defend anything, just that men are probably not always aware of the problems women face even in the west so be vigilant when you ride public transport and don't think it's only a Japan problem.

the problem is that complaining and making a fuss about things that bother you is frowned upon. especially for women. so they suffer in silence. and the games probably are mostly made by men, who of course don't think it is as much of a big deal. not much different from what it used to be in the west. if only samurai chivalry was more prevalent. but unfortunately keeping appearance (and not embarrassing others) is more important.

The RGG games are pretty open about widespread societal problems in Japan. Indeed, the game before the current one had a pretty humanistic depiction of sex work that was not at all glamorous or lecherous.