There's a bunch of claims in the article that are misleading or just wrong.

> Core rail operations are profitable for every Japanese private railway company

Only the urban, legacy private railways that benefited from the "build a suburb and trains to it" system. Rural lines, private or not, all hemorrhage money, as do many of the newer private lines (often built by government and private only in name).

> Japanese cities have the lowest residential density in Asia

This is because Japanese "cities" (市) are administrative units, not actual cities. Particularly in the rapidly depopulating countryside, it's common for a bunch of dying villages that can't afford to duplicate their services anymore to get more or less forcibly merged into a "city" like Miyoshi in Shikoku that, in satellite view, looks like untouched forest:

https://maps.app.goo.gl/tRtdQisJCUMsqivv7

> The urban area of Tokyo, the densest Japanese city, has a weighted population density less than that of many European cities,

This is only true for Tokyo Prefecture, which encompasses a vast slab of mountains. Actual Tokyo (23-ku) packs in over 15k people/km2, 50% more than inner London (10k) and nearly 2.5x Greater London (6k).