I have been living in the inaka for 8 years now and I always laugh at this kind of articles. They only focus on the core areas of Tokyo, Osaka, and a few big others cities, and forget to mention that outside of those areas the whole country is just endless urban sprawl of the ugliest, soulless cities you can imagine.
This article is specifically about its most livable cities. Why would you expect them to discuss the cities people don't want to live in? Every country has plenty of these. The point is to show the things that make a place livable, not to show all the ways a place isn't.
I wouldn't say it's the vast majority if Tokyo/Chiba/Saitama/Yokohama holds like a third of the population. Add in those other cities you mentioned and the majority of the population lives in cities.
Of course in any developed country the majority of the population lives in cities. What I mean is that Japanese cities, outside of a few core areas, are really ugly and depressing.
People are forced to go to the big cities for economic reasons and not lifestyle reasons. Unlike America, it’s not just white collar office workers who must relocate to urban centers. This concentration forms a feedback loop.
Unfortunately my workplace is in the countryside. Someone decided it was a good idea to build a big international research center in the middle of nowhere. Which is now a liability for the project, as few people want to come work here.