Eh. I feel like this conversation is lacking basic statistics.
San Francisco: 18,451
Tokyo: 16,000
San Francisco is not all that high, but denser than Tokyo. Cities don't need to be high to be dense. That's one of the biggest misconceptions. Most of the world's high density cities don't do so by using skyscrapers.
The actual problem? I think it comes down to two factors:
1. Almost all density in NA was built pre-car
2. So density is limited by the size of areas that were built in the pre-car area.
Taller buildings isn't necessarily the answer. Narrower streets is a larger determinant of density. But it's very hard to tear down streets, make them narrower and add new buildings.
It's especially hard to rebuild the suburbs around cities like San Francisco and make them more San Francisco-like. If the whole Bay area was built like SF, there would be no silicon valley rent crisis. Yet for some reason everyone focuses on SF.
I'm writing this in Montreal, a city built like SF. It's infuriating that this whole debate happens without people googling density stats.
How many people would have guessed that SF is denser than Tokyo, per square mile? Tokyo is bigger, and holds more people, because the Japanese have sensible zoning. But "tall buildings" is not how they do it over the whole span of the megalopolis.