The author mentioned that keeping those railways around, instead of just getting rid of them for cars like the US did, allowed the cities in Japan to become that dense in the first place. It's not because Tokyo and Osaka were always this populated. Even then,

The urban area of Tokyo, the densest Japanese city, has a weighted population density less than that of many European cities, including Paris, Madrid, or Athens.

Of course there are plenty of people who live in Tokyo proper, like I do, but most people I know actually live on its periphery, where the density isn't as crazy.