Many small business like this are also run by retirees who want to meet people and bring some value to their community. It's legal to run a small business from a certain percentage of your ground floor in any location in Japan.

It also doesn't have to be your primary source of income. If you can run it from a structure like this you could just operate a cocktail bar on the weekends. Even in the US I know of a small pizza place that offers takeout only on a few days each month and it's operated out of the owners mom's kitchen. Not sure how legal that is and turning that inti a sit-down place would certainly be an issue.