From CAHSR:
"The San Francisco to San José project section differs from others because state legislation defined the alignment. Per the requirements of Senate Bill (SB) 1029 and regional multi-agency agreements, high-speed rail service along the San Francisco to San José corridor will be a blended service with Caltrain and high-speed rail service sharing tracks."

and

"The alignment includes high-speed rail stations in San Francisco, Millbrae, and San Jose; construction of a light maintenance facility (LMF) on the east side of the Caltrain corridor in Brisbane; and improvements for safety and speed to allow for operations at a maximum speed of 110mph."

That latter implies grade separations will proliferate. To get above 110, even to 125 would be a bit heroic and require the taking of quite a few dwellings.