Not a local, but in my experience this is due to tourists not being able to speak Japanese, which makes the people working in a place very uncomfortable ("will this person follow the rules? How can I do proper service if I can't communicate?"). A 大丈夫、少し日本語をしゃべります (it's ok, I speak a bit of japanese) has been enough to open the doors for me.

That being said, they do have issues with some nationalities. For example, the average American is way too loud for the average japanese place. Even if they think they are being polite, they just talk too loud and too much for japanese sensibilities.

Oh definitely. I mean, my neighbourhood has a bar that doesn’t even allow people who don’t live in the area as well. I guess, the gay bars not allowing foreigners is for a different reason, but soft discrimination is very ubiquitous. On the bright side, there are hundreds of thousands of other establishments that will happily take your money.