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.
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.