Not entirely sure what you’re saying but I’m literally, actually, living here and have been for 20 years. I’ve lived all over Tokyo and indeed elsewhere in Japan. I know what the air is like where people are actually living and working, as opposed to wherever the monitors happen to be placed.
There is loads of research showing a marked drop-off in the danger to humans from vehicle emissions as you move away from the kerbside. Even walking on the far side of a wide curb can significantly improve your prospects. My point here is that people are living in extreme proximity to tailpipe emissions, all day long.
It is a perfect candidate - perhaps the best candidate city in the world given how much else it gets staggeringly right on urban design - for strict tailpipe emissions regulations. Ban diesel trucks, introduce congestion charges, incentivise the adoption of EVs.
That is unlikely to happen, however, as Toyota in particular famously is one of the biggest global lobbyists for the internal combustion engine - a fact covered numerous times at length here on HN. That’s a fascinating political and economic story in its own right and one I’d encourage people to read up on.
Tokyo’s air quality is a story of corporate and political greed. Nobody does anything about it because no one talks about it.