I have friend living in Tokyo paying <10万円 in rent for a (very small) single unit. A couple other friends share a larger unit and pay similar per person. All are in the 23 wards. This is unimaginable for other friends living in Paris (one of the 20 Arrondissements) and New York (one of the 5 boroughs), regardless of size. I have no anecdata on London.
Regarding size, I was far more comfortable living in a ~550sqft 1LDK in Japan than I ever was in 800sqft-1000sqft apartments in North America - everything is geared to living in tighter quarters (from furniture to fridge to food packaging) making it much more convenient than trying to fit a full size couch into a small western apartment, or trying to save by bulk buying ingredients when you don't have the space to store it.
So I think the title of the article is half right (rent is cheaper than you'd think), missing some key info (wages are also cheaper than you'd think), half of it is roughly incorrect (housing is not any more spacious than you'd think), and the article itself doesn't back it up well.