Well and there is also the old Bart tunnel and more modern Central Subway. And then there are the subway tunnels they have built/building in Los Angeles.

Snippets I've read over the years seem to say that subway tunnels and deep foundations don't tend to fail in earthquakes because they to move with the ground around them. And because they are already structurally strong.

Basically the lack of mass transit to support higher density is because of lack of willingness to pay for it. Unwillingness to pay for public infrastructure is due American economic ideology. Not anything specific to San Francisco.

Shitty soil and earthquakes in combination is a bad combo.

https://www.businessinsider.com.au/earthquake-expert-san-fra...