That's mostly just because Tokyo is so immense: Greater Tokyo is the world's largest city on most measures. However, the skyscrapers are concentrated in a couple of districts, and the vast majority of the city is indeed low-rise (under 10 stories or so even in the immediate city center, under 5 outside it).

Incidentally, most urban planners figure that Tokyo should be more dense instead of forcing people to endure multi-hour commutes, but strict sunlight laws make it very difficult to build tall buildings outside a few designated areas.

Well, in proportion. Tokyo has almost double the population of the world's second largest city, too.

The proportion of all interior space in Tokyo above the 20th story of buildings is infinitesimal.