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
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!