I understand that to be one of the differences in approach to zoning, zones and buildings are considered on a spectrum of "impact". A high impact building like an industrial plant shouldn't be too close to low impact buildings like a single dwelling. But because it's a spectrum you get a natural mix of low, medium, and high impact buildings. A large residential complex might be considered medium impact and so can go next to a shopping complex that is also medium to high impact etc.

I would imagine that a great deal of Tokyo's megalopolis fits nicely in the medium impact zone, allowing housing, small scale manufacturing and commerce to mingle in an organic way.