Kalzumeus spoke about "Tokyo" to represent Tokyo, Osaka, Nagoya and other large regional cities.
As you might expect, these Tokyo-like cities are much more expensive at their centre than at their periphery. Nevertheless, I imagine your eyes may water when you find out just how much more so. I only know one of these cities well, and to be fair only in land values not in rentals.
In absolute amounts, Tokyo itself is of course more unequal than smaller big cities. But the relative value distribution is perhaps fairly consistent across Tokyo-like cities.
Within Tokyo-city, very central regions (Minato-ku) are valued at 4X over central urban districts (Nakano-ku), which in turn, are 8X more expensive to buy than the least valuable outer-Tokyo districts (Hachioji-shi). So there's a 32X differential in land values within that city's borders.
Now, let's zoom out from the city itself. Within just a few hours drive or rail journey, we can easily get to 300X land values: $300 in Minato buys the same area of land worth around $1 in a fairly central district of a fairly large town in Nagano. Parts of mountains obviously go for much cheaper than land in these towns, but I don't have good market data for that. My guess is a further 5X - 10X.
Undoubtedly, it is more than 1,000 times, and perhaps sometimes as much as 10,000X, more expensive to buy a plot of land in Japan, than another plot of the same size just 500Km - 1,000Km away.
One may reasonably dispute these figures in detail. I did try to be conservative. Nevertheless, they are certainly right in the order of magnitude.
Getting back to your point, I would say that in spite of the wonderful societal benefits of world-class transportation within and between cities, if the goal was to achieve ball-park economic parity across the regions then that policy in Japan has been a failure. Income & expenditure? Sure ... all of Japan looks pretty consistent. Property valuation? ... the discrepancy is almost unfathomable.