It's valuable to be next to useful places. This value of proximity could be increasing so rapidly that it would wash out the value of any particular residential building you could put there.
As the article points out (but does not emphasise), the houses in Japan are by design transient. They are built to fit need, and demolished to make space for something new in their due time.
This makes the land much more valuable - a plot can be repurposed when necessary, especially when the zoning rules and taxation encourage it too.