But isn't rent in Tokyo still disgustingly high? Something doesn't add up.
But apartment buildings in Tokyo are terrible. Fifteen years is considered "old" and that's not due to high standards - it's because after fifteen years the building is falling apart. I also suspect that if you compare rent per square meter, you're right you'll still have higher prices than London at least and probably SF as well, but significantly cheaper might be a stretch. $2500/month for 500 sq ft is expensive anywhere.
(And if the rent doesn't get you, parking will, though it's very easy to live without a car in Tokyo.)
Nowadays I'm living in London and have seen housing for way higher prices and way, way worse condition than the apartments I've seen in Tokyo. London build quality is utterly terrible. Japanese build quality is quality.
And even if it was, it still adds up. Rent in Manhattan is ridiculous. But you still find abandoned houses all over Detroit.