It's not as flat as it looks on a small-scale relief map, nor as straight. And it's along the San Andreas fault the whole way, including the "creeping" part and the Parkfield/Cholame area where there are M5-7 earthquakes about every 25 years and where the 1857 Big One in SoCal seems to have started. All things considered, I'd rather be crossing the fault, designing for inevitable displacement in a short segment, than running along it with much more damage possible (including ongoing damage in the creeping segment).

SP wasn't being dumb when they gave up at Tres Pinos and headed for the Coast instead. Coast is definitely not HSR territory, though, with all the mountains to cross and only lightly populated towns along the way.