More like a "lack of zoning". Japan's very limited zoning restrictions allows more natural cities to be built. Additionally, the train companies own the land a

More like a "lack of zoning". Japan's very limited zoning restrictions allows more natural cities to be built. Additionally, the train companies own the land around the train stations and are thus encouraged to develop the land for commercial use, effectively setting up destinations for the users of their train systems. The cities then develop around the train stations as the primary hubs of commerce.