The reason I brought up the areas surrounding train station stops is because those areas are the prime commerce locations where things are supposed to be at their best. Things like homelessness exist everywhere in the shadows of society. To have buildings that contrast sharply with the glittering skyscrapes that symbolize Tokyo exist adjacent to train stations is a signal that not all is well everywhere in the country, even within greater Tokyo.
That happens to be a wrong assumption. Homelessness happens mostly in the most expensive areas of Japan, which are roughly the same as the prime commerce locations.
In terms of housing and basic needs, rural Japan is far ahead. But this doesn't happen just in Japan, it's a common theme. If all you aspire to is a full time job and a modest life, it's easy to have just that in many small towns in Japan where literally only the mentally impaired may need support to achieve just that. But a lot of people are addicted to urban life, and urban life in Japan is tough.
However, if Africa is third world and the US first world, then Japan is one better, in most respects, perhaps, zero'th world.