In the first link in the original post, among the many datasets available in Japanese there is a resource from the Ministry of Land, Infrastructure and Transport that provides geocoordinates for addresses in most Tokyo wards and cities. The resource is
http://www.data.go.jp/data/en/dataset/mlit_20140919_3059
For example, there are around 178,000 building addresses for Setagaya ((世田谷区), population 900,000) which would seem comprehensive [as a single building can house anything from 1 to over 100 people], although I cannot be sure it is a complete list. I also note that some cities in the outskirts of Tokyo (e.g. Chofu 調布市) are not listed. The dataset for each city/ward within tokyo will give you four items of address data - machi (listed in japanese characters) = name of 'town' within the city/ward, Chome (i.e. district within the machi, usually a number from 1 to 12 listed here in Japanese characters), Gaiku (block number, as a number from 1 to about 50) and Bango (building number, again a number from 1 to about 50), as well as the geo-coordinates.
PS If anyone can give me a link to a similar dataset for Chofu, Tokyo (調布市) I would be very grateful!