It's my understanding that houses in Japan are zoned to allow a percentage of the space to be used for a low-impact business, like the coffee shop in the article, and that bigger businesses are allowed on the bigger roads and in dedicated commercial/industrial districts. Also most houses can be converted to triplexes, too. This helps with density, encouraging more businesses nearby, less need for cars, better quality of social life, etc.
I see what you mean about the potential for abuse - maybe Big Money would buy all the houses and run small businesses from them? But regulations or taxes could be used to dissuade them. Theoretically, anyways.
I wondered if Japan does anything along those lines to avoid the problems you mentioned, but google ain't what it used to be and I wasn't able to find specifics.