That's a great blog post. As I understand it, the national law is just as described, with only 12 zones, but the localities have some latitude in how to apply the law and make some blanket restrictions about things like building height. For instance, Kyoto famously has very strict limits on building height, though this is biting them in the ass because it keeps them from creating enough density to get more tax money, and too much land is occupied by religious sites that don't pay any taxes at all, so the city is going bankrupt.
related: https://en.wikipedia.org/wiki/Japanese_land_law
Looking it up, I see you're right. They have national zoning laws but even there, things do seem to be getting more complicated.