I'm so confused by the idea that Tokyo is somehow bike-centric. Perhaps there's another Tokyo somewhere in Japan that is not a subway-and-taxi centric metropolitan area where bikes are rarely seen.
It's a pedestrian-friendly city, though, I'll give you that.
Keep in mind that "Tokyo" isn't just the super dense, most central area of the metro. Tokyo technically covers a huge swathe of land, including towns that are basically suburbs. And while Japanese cities don't usually include much bike-specific infrastructure, in practice many of the narrow roads are pretty bike friendly anyway, just due to their very narrowness.
I have spent a ton of time in Tokyo. I am fascinated by this. I actually suspect they are including the delivery bikes, which are not really the same thing, and the cited study, which I will try and track down, has poor data hygiene.
It's not that small towns are strung out along roads. Rather, the town itself becomes a nexus for walk/bike-ability. Instead of every trip to the grocery store, movie theater, and gym being taken by car, the vast majority of trips are taken by walking or biking. This isn't to say there aren't cars in town: on the contrary, roads exist, ideally going around heavily trafficked areas. This lets the roads focus on being roads (getting people from place to place) and the streets focus on being streets (allowing people to walk, bike, and "experience the world", in the parlance of "Not Just Bikes".
Of course, the next town over (let's say it's 20 miles away) will be "down the road", with a both a road and a train connecting them.
