I could see having CAHSR *not* involved with Altamont as a plus. If it's done primarily as a regional line, it can be built to reasonable standards for that purpose, yet still fast enough to qualify as minimal HSR. If the *real thing* ever gets built, a "triangle" or "Y" system that covers SJ-SAC, SJ-Merced, and SAC-Merced could be done that makes good connections with the HSR main line (should that ever happen) or the Valley appendix (making it more useful than if just running a few Amtrak trains). IIRC, a Sac extension from Merced was in the original plans, for a later (indeterminate schedule) phase. But if it's not part of CAHSR it doesn't have to be built to 225mph standards (cutting the cost drastically) - merely 150 is sufficient.

Even with a Dumbarton crossing to shortcut the line a bit, though, I don't see how a trip from SF via Altamont would be quicker than a trip direct via a line meeting similar standards and a transbay tube. The Cal-P route (or something near it) is shorter SF-Sac than Altamont. Unless you assume that it'll never be improved. But Sac-SJ is definitely shorter via Altamont, and much of the countryside is more open and easier to build on; get rid of the slowness of the current Pass and Niles Cyn and it becomes a(n iron) horse race.

Either way, I'd like to see trains from Sac and the northern SJV that go to the airports in the Bay Area - either direct or with dedicated connections, and space for luggage (maybe even remote checkin?). SFO/OAK/SJC would probably love that; SMF would fight it tooth and nail. But it needs to be done. BART isn't sufficient. Maybe mollify SMF by extending the line to a terminal at the airport rather than just downtown Sac, like the Europeans do?