Most of the SP branch to Santa Rosa was abandoned in the 30s. I remember the remaining ex-SP trackage in Santa Rosa, as my grandmother lived in that part of town around 1960. I suspect it was abandoned when they built the US101 freeway (if not before) as the freeway would have crossed it.

As for them not using the SP route as a shortcut to Schellville, bear in mind that there was still quite a bit of traffic on the NWP south of Santa Rosa and (probably more important) that there was still the Santa Fe barge connection at Tiburon. By the time things changed in Marin, the SP branch was long gone.