There are almost certainly other mechanisms that keep Tokyo’s land and housing affordable for the average Tokyoite and that allow the city to grow to such a large size.
Tokyo is a large complex place and it is difficult to truly understand another culture. But I would guess the following are factors in Tokyo’s success.
Japan has a unique planning system. Zoning is a national law not a municipal by-law, there are only 12 types of zones and the zoning is maximal -in the sense that areas that zone to allow nuisance activity -say commercial office blocks are also zoned for, anything less of a nuisance on the zoning scale -such as apartments, or stand alone housing.
Japan has a culture of engineering excellence and teamwork which makes seemingly impossible tasks possible. The punctuality of the train network is legendary. Below is a video demonstrating the ability of Japanese engineers to implement system changes -in this case changing an above ground train track to a subway track in under 4 hours.
And here is a description of a system Japanese engineers have developed to improve reliability and minimise error.
Why Japan's Rail Workers Can't Stop Pointing at Things
It is hard to miss when taking the train in Tokyo. White-gloved employees in crisp uniforms pointing smartly down the…
Private railways are a pragmatic mix of public and private features. The private features are well documented. The public ones less so -private rail companies can request the government uses its powers of compulsory purchase to acquire land for new rail corridors (see here why this is important) and the private railway companies can access low interest loans from the government. Unfortunately, the details of this government cooperation is hard to find.
Private railways in Tokyo are involved in property development and commercial enterprises -residential housing on the periphery, commercial development in the centre -including competing department stores! These commercial property activities can provide 20–30% of the revenue for private railway companies. Probably initially private railways would want more residential development on the periphery to build up a customer base, later they would have also want commercial development in the centre -such as restaurants, shops, gyms, movie theatres…. to create trip attractors.
One urban planning mechanism I question is -in the past Tokyo expanded greatly on its periphery and I wonder if Japanese urban areas still have this freedom? If Tokyo has this development option, even if not greatly used due to the city going through an intensification phase, this option may help reduce land speculation -the exploitation of economic rent (Landblog article on economic rent here). There is definitely evidence from affordable cities in the US and Europe, that cities which have the option to grow both out and up in a less restricted manner, do not experience as much land banking and house price inflation. It is possible in Tokyo that a car-based urban sprawl development model is in competitive tension with a private railway based housing and commercial intensification model. Although, so far I cannot find evidence to support or refute the possibility that Tokyo can develop outwards without restriction/rationing. Therefore I am unsure if this competitive tension idea is true or not.