I've been to Tokyo (and it's awesome!) but I don't live there.

I've only glanced at the headlines of the article you posted and most of the factors appear to be in the article. There are a few things that are missing though, afaiu, and it really is a bag of mixed blessings:

• fairly relaxed building codes which means building gets cheaper
• average houses, especially if they're on the smaller side, are only a couple of decades old -- the Japanese demolish and replace their relatively cheap housing fairly often
• less space for motorized traffic
• not a lot of greenery

Cursorily related to the final point: I was also really shocked at Japanese parks. On the plus side, they're extremely neat. However, most of them have super-wide ways, so half the park is just paved over. And of course there are opening hours, usually they're open until 6pm but they have all kinds of alarms and announcements going off in the 30 minutes prior.