I’ve only visited once, but my impression of their urban areas was that Japanese zoning laws and planning permit are very different to even UK ones, and worlds apart from American ones. I assume there’s some centuries-old historical reasons that I’m just not aware of.

There are residential houses sandwiched between restaurants, perfectly legitimate businesses built on top of some ‘perfectly legitimate’ businesses and underneath other even shadier businesses. This definitely means that any district with a focus on entertainment will often seem sketchier than it really is.