The article doesn't go into detail - are people in Japan likely to own both the house and the land? Or just the house and instead have some lease / permit for the land?
The land value is assessed separately from any structures built on it for the purposes of taxation, which I think is what they mean when they say it is “calculated separately”.
Most people for houses own the land and building.
These are assessed separetly for taxation purposes/assessment value.
Some areas are leased land for say 75 year contracts or any other long term (alot of indigenous/native owned land that is leased for a term contract. There's some condo development and mall with a 100yr lease etc)
Here's one I found that actually looks looks pretty nice for ¥3M (USD $21K). But the lease payments and administration fees probably scare away any prospective buyers (it's also in a forrest in one of the snowiest areas of Japan, so accessibility in winter might be a bit of an issue).