I think it's important to realize that, and it's mentioned in the video linked, individuals staying in these apartments are making a deliberate choice so that they can have a better commute.

I've lived in central Tokyo in a rather large 1BR running ~$2,300 per month and now reside a bit further out paying ~$1,600 for a smaller 1BR.

Many people in Tokyo live ~45 minutes commute to work (via admittedly crowded trains) and pay significantly less for reasonably sized studio apartments.