Thank you for the links, they were very informative. I also found the article a bit cursory. I was particularly surprised that they didn't mention Japan's construction industry. It makes up a much larger part of the economy than in countries like the United States or the United Kingdom, and it exerts a lot of political power. A large number of the laws promoting new construction over renovation or purchase of existing buildings benefit the construction industry more than property owners.

I recommend Alex Kerr's Dogs and Demons for a more detailed discussion of real estate and zoning laws in Japan.