The basic problem is that there are a lot of small patches of lands in Tokyo that are too small to build a normal flat (recall that a patch of land is very, very expensive in Tokyo and you cannot just buy an adjacent land to expand it). Until recently, these small patches were left vacant since there was really not much use.
Recently, due to lots of cheap money floating around, some speculative developers (Spilytus, referenced in this article, is one of them) try to utilize these lands, by building such micro housings.
So it is a relatively new thingy pushed by supply side speculators and I honestly do not think these small housings have so much popularity among actual dwellers as this article suggests.