No matter how you plan to go from SF to LA, you have to cross many faults, with the guarantee that if what you build lasts long enough to maybe pay off the capital cost (say, 50-100 years) you will have to survive and recover from a major earthquake. Bay Area segments have to deal with bay mud/deep alluvium and the Hayward-Calaveras system, which is a more likely source of problems than S.A. in the near term. If you go down I-5 you have to deal with both ground subsidence due to groundwater depletion (has caused problems with CA Aqueduct over the years) and thrust faults along the southern (especially) Coast Range front (Coalinga, Kettleman, Buttonwillow areas for instance). SJV in general has very deep alluvium that can react in interesting ways to even fairly distant large earthquakes. No matter how you go over or through the Tehachapis, you have to deal with the White Wolf system and active folds (like Wheeler Ridge, San Andreas (Gorman area for straight shot, Palmdale area otherwise), and Garlock system (mostly just on the Palmdale route). The San Fernando Valley & LA area in general is of course not immune to strong shaking and occasional ground rupture from local faults (cf. Northridge, Sylmar, Whittier, Long Beach, etc etc).

There have been several articles pointing out that the Kern Canyon fault is anything but dead. The Corps is considering that in studies for strengthening the dam; K.C. fault barely misses the main dam at Isabella, but close enough. Several other papers theorize on micro (and sometimes not so micro) earthquake alignments suggesting that the White Wolf is evolving into a Garlock replacement. Fun stuff. Great place to put a major public works project that has to be practically unconditionally safe (given modern legal environments). It's an engineering problem, and expensive, and not guaranteed in any way to avoid damage.

HSR trains will operate at the speed of a prop airliner, or a jet on approach or departure, and with the passenger load of a 747 or A380. And no seat belts? Engineering is critical (and expensive) to make sure that everything works right not only in ordinary operations but in emergencies. Granted, a train may not fall out of the sky (but what if a bridge breaks?), but bad things can happen anyway that need to be designed around. The speeds being discussed for typical HSR equipment and loads hold a lot of energy. The design will happen, but some things done in planning can help make the design easier and more effective; relaxing the time standard would help, but won't happen.