In this case the problem (other than weather) was 100% infrastructure: many of these roadways are built below grade, which means that when it rains, they flood. Floods are generally not part of the threat model for Bay Area infrastructure (though perhaps they should be), so when civil engineers trade off drainage vs. earthquake safety vs. land use vs. traffic, drainage is usually the first thing sacrificed. The mid-peninsula had 5 consecutive avenues underneath El Camino & the Caltrain tracks washed out; most of them have been recently rebuilt as grade-separated underpasses as part of the Caltrain electrification project, so that traffic would not need to cross the tracks. They probably would not have flooded as at-grade intersections.

Arguably this was the right choice, as everybody just stayed home during this storm, so real impacts were relatively light. By contrast, Bay Area traffic is a disaster every rush hour, so getting a few folks to take Caltrain instead of driving or avoiding just one collision on the tracks already puts you ahead of the cost of this weekend's storm.