It's fine if the places where 80% of people live are walkable and the rest maybe aren't as great.
And in any case, I am from Spain, a country were even small villages a pretty walkable. There was an article here recently explaining it: https://news.ycombinator.com/item?id=38189840
I don't know about that. My experience (in the UK) is small, rural places are by default walkable 'cause they haven't changed that much in the last coupel of centuries, when you had to be walkable since cars and bikes didn't exist.
There is a high likelihood that the old town square has been taken over by local government offices. If you work there great, but otherwise not the type of place you would visit often if at all.
In short they still have the walkabel guts from the 1800s, but there is nothing to walk to.
If we go back in time to North America in the late 1800s, for comparison, it's much the same. People didn't have cars, and while some people had horses, they were expensive and not everyone did. The towns had a railroad station and otherwise were very walkable. There were no parking lots forcing low density because there were no cars.
Edit: note that I don't mean to imply that all smaller towns or cities in Japan are like this. The boring towns that are copies of suburban America are places I simply wouldn't visit, because there's absolutely nothing interesting there for a visitor (just like suburban America); the towns I've visited are interesting, cute towns in the mountains that actually attract tourists for some reason (onsen, access to mountain trails, etc.).
Source: 5 years living in Aomori.