So here’s a quick rundown of how the decentralisation mentioned in the article is structured: Japan is split into 47 todōfuken (都道府県), their closest analog to a US “state”. You’ll hear these called “Prefectures”, but just like the US has states (Washington) and territories (Washington DC), Japan only has 43 prefectures, the rest are technically different types of district. Tokyo is (the only) “metropolis” region directly under the national government.
Across Japan every local district is split up into shichōson (市町村), cities, towns, and villages.
“Central” Tokyo is a special area where that standard shichōson system doesn’t apply, except really it does, we just call things “wards” instead.
Every local district, whether city, town, village, or ward, is essentially the face of government in that community. They provide public services like sanitation, education, and community engagement events. When it’s time to vote, you will go to your local [city|town|village|ward] office and do it there.
These local offices have quite a bit of power (and are what people are talking about most of the time when they refer to the “infamous” Japanese bureaucracy. For an excellent film looking at this world, I cannot recommend Kurosawa’s “Ikiru” enough. I believe it’s in IMDbs top 10 of all time), while they are often ridiculed for being slow and stuffy, they are a very real check and balance against the prefectural and national governments.
Tokyo has a city-wide government (analogous to a state government) that is politically important at a national level, an example of the more illustrious institutions run by this level is the famous Tokyo metropolitan police.
As the article stated, Tokyo is rich. 10th largest gdp nation in the world if it was an independent nation, this means there’s a lot of money flowing through that city government. Depending on who you ask, this is the level that shady deals, and blatant corruption happens most. The tabloids are always busy in Tokyo.
The point is, all these powers seem to be quite well-balanced, and the citizenry engaged enough to keep them in check, in other words, like a well functioning democracy. I’m not saying it doesn’t have its downsides, and I’m no fan of Tokyo after living there for four years, but it is a remarkably well-working system. I’d still rather be in Osaka, or better yet, the countryside tbh.