Zoning, as the article mentions, is one important element. I think there are others. The excellent transit system, and cultural acceptance of small homes for example.
I think these articles should explain difference between Tokyo and Seoul. South Korea basically copied Japan's zoning system, it is inclusive, central, etc. and Seoul has excellent transit and Koreans are (although not to the extent of Japanese) fine with small homes and high density. Still Seoul is nearly 2x as expensive as Tokyo.
Good points. I wonder to what extent the Japanese real estate bubble pop of 1992 played a role. Housing in Tokyo was sky-high in 1989, to be sure, despite their zoning rules being enacted in 1968.
