The problem is instead entering and exiting the Valley. The HSR line will cross the Calaveras Fault when going through the Pacheco Pass (between Gilroy and Merced), the seismically active Tehachapi Mountains between Bakersfield and Palmdale, and the San Andreas Fault between Palmdale and LA. The San Andreas also runs parallel to the tracks between San Francisco and Gilroy, at a distance of 10-15 miles to the west.

California's urban geography evolved around the rails, something you can still see when riding the passenger trains here in the state. It would not take a great deal of effort to expand rail here in California - it just requires money and the political will to spend it.

Even we here in Monterey evolved as a railroad town. Founded by the Spanish as the capital of California, our fishery and tourism industries emerged after the 1870s when the railroad from SF reached here. Passenger rail service ended in 1971, but the ROW and even the station here in town have been preserved and are now publicly owned. Monterey County is studying a light rail plan to connect to the UP Coast Line at Castroville, where it will meet with a Caltrain extension to Salinas.

Prop 1A contains $950 million for non-HSR passenger rail that connects to the HSR system, which could well help restore more robust passenger rail to Monterey County. The Gilroy HSR station would be less than an hour away by car or train...

And the world will live as one

This is of course based on pure ignorance.  The bigger a project the more likely it will have the most state-of-the-art earthquake safeguards, which are tremendous.  Earthquakes are simply not a concern for a project like this.  If a quake occurs and the tracks spread there will be immediate breaks put on all running trains.  After the quake you fix the tracks.  It's not really a huge deal.

Tall buildings, for the record, are built with counter-weighting and shock absorption that makes them far safer in an earthquake than your new McMansion.