Japan on Wikipedia, stats:
- Area: 377,972 km^2 (145,936 sq mi)
- Population: 126,740,000
- Density: 336/km^2 (870.2/sq mi)
- Area: 423,970 km^2 (163,696 sq mi)
- Population: 39,250,017
- Density: 93/km^2 (240/sq mi)
The United Kingdom:
- Area: 242,495 km^2 (93,628 sq mi)
- Population: 65,648,000
- Density: 270.7/km^2 (701.1/sq mi)
- Area: 238,397 km^2 (92,046 sq mi)
- Population: 19,638,000
- Density: 84.4/km^2 (218.6/sq mi)
California makes for a good comparison, as it is only a bit larger in area, with less than a third of the population. Yet most of the population of California is in the greater metropolitan areas of Los Angeles, San Jose-San Francisco-Oakland, San Diego, and Sacramento (about 33 million combined).
Or compare to Sud-Muntenia in Romania. That's the administrative division in Romania around Bucharest. If we combine Bucharest and Sud-Muntenia, we get a population density of only 149/km^2. That's less than half the population density in Japan. Yet Bucharest is easily the biggest city in Romania, much less that area. Why do Romanians squeeze themselves into just one city?
The densest "city" in Japan according to your source is Osaka/Kobe/Kyoto at 38th. Bucharest doesn't even make that list, despite having an eighth of the population of Romania in it. London makes the list at 43. Why does the UK pack itself into just a few cities? Both the UK and Japan have five cities on that list even though the UK has half the population and a lower density.
Japan has a lot of people and not that much space. Yet it's not significantly more prevalent in the highest population density list than the UK, with half the population. The actual city of Bucharest itself has a higher population density than any of the metropolitan areas listed in Japan. Yet Japan has six times the population and four times the density of Romania. California has a third as much population and still appears on the list three times (and we could get that up to five if we added Hawaii and Nevada).
I don't think that Japan is that exceptional in this area. Further, I don't think that this is really caused by political factors in Japan. The primary issue is that Japan has a lot of people and few places to put them. This leads to high density in those places that are suitable for building. Particularly as Japan is in an earthquake zone and needs to be extra careful in its building. It can't just build on the side of a mountain. This restricts it from using some of what land it does have.