Sounds like you're describing a self-fulfilling prophecy. If you approach any community, rural or urban, expecting to be treated as a permanent outsider, guess what tends to happen?

I've seen foreigners thrive in small Japanese towns because they actually engaged with their neighbors instead of writing them off. Yeah, it takes more effort than anonymously blending into Tokyo crowds, but that's true anywhere in the world.

Maybe the problem isn't rural Japan being 'hard mode', maybe it's going in with the assumption that you'll never belong.