People invoke Aum Shinrikyō all the time to draw conclusions about the condition of Japan at the time and the wider sociological forces that led to its rise. People invoke the existence of the tiniest, most fringe right-wing groups to draw conclusions about Japanese attitudes as well.

But I'm not even claiming the NSU, or even its allies in the state apparatus, are representative of the attitude of the average German, which are of course very liberal by historical standards—what I'm saying is that despite Germany being a country where the police forces are penetrated by Nazis operating in coordination with murderous terrorists and where right-wing groups were able to mobilize a riot with thousands of participants in Chemnitz alone, none of that stops millions of immigrants from leading peaceful, happy lives in Germany, despite the real, even violent, dangers that some of them face.

In comparison, a stranger not wanting to sit next to you on a train sounds like a very trivial problem—a very first-world problem. And yet, it's enough to cause you to dismiss Japan entirely as some inhospitably xenophobic society, even though there are immigrant communities in the countries that you've lived in who can complain about much worse. I'm sure you've seen the videos of people screaming racist abuse at passengers on the Tube—would it be fair to conclude that Britain is so hostile to immigrants that I shouldn't even consider living or working there?

My contention is simply that the experiences you've described are hardly adequate to demonstrate that Japan is uniquely or exceptionally xenophobic, and it's bizarre to conclude from that alone that it would be difficult to establish a happy life there.