The transit part is key for Tokyo, everyone talks about how housing supply is robust, zoning is loose, density is high and unit sizes are small; but few talk about how having 130 rail lines with pervasive express service means that there’s an enormous amount of land within commute distance.

Set this charting tool to Density, plug in Tokyo with a number of other major world cities, you’ll see the effect in the data.

https://jnolan.shinyapps.io/Population_density/