The picture below shows us what may happen in the Bay Area whenever the CHSRA obtains further funding.
You say, no? That it won't happen because elected officials, Simitian, Eshoo and Gordon have negotiated an at-grade two track solution as part of "phased implementation" for the Caltrain corridor on the Peninsula? That there will be two track sharing among Caltrain, the High-Speed train and Union Pacific freights? Do you actually believe that?
Rest assured that there is a determination on both the Caltrain and the CHSRA's part to have four tracks and to elevate them in order to achieve total grade separation. From an engineering standpoint, elevated viaducts, such as the one pictured here, are the most cost effective solutions wherever multiple grade crossings are in close proximity.
PAMPA is just such an area. (Palo Alto, Menlo Park, Atherton.) There are ten grade crossings. Leaving the tracks at grade would require ten street underpasses to be constructed and the costs would be enormous, with many eminent domain adverse takings in the area surrounding the crossings and the necessary under-passes.
Meanwhile the viaduct elevated track alignment permits a flat/level track for as much as possible of the entire 50 miles of Peninsula, has a smaller on-the-ground footprint within the existing rail corridor, and permits many adjustments to curvature, thereby minimizing them.
And, since when did the CHSRA indicate any abandonment of that end-state elevated four-track solution for the corridor? Their acceptance of the interim at-grade two track solution (if indeed that is the case) is totally predicated on not having funding -- but only for the time being -- for the elevated four tracks.