They would have to build new track across the California Coast Ranges[1]. Mountain crossings are expensive and difficult, and mountain crossings that need to maintain the curve and grade requirements of HSR are even more so. The crazy cost overruns for mountain crossings (this one and the Tehachapi Pass) are what killed the project.

This new de-scoped HSR project is basically "the part of HSR phase 1 that doesn't require us to cross any mountains". In California that's obviously very limiting.

[1] https://en.wikipedia.org/wiki/California_Coast_Ranges