First, thanks for the link to the draft. Amazing how the simplest solution is rarely considered by planners. Years ago, Caltrain supporters proposed a BART infill station at Shinn St where they overcross the tracks used by ACE. Essentially zero feet of new "guideway" just platforms, elevators and escalators. Why is it better? No need to divert trains to Union City; thus greater frequency options because all trains could offer connections to BART. This design also allows for network connectivity using Centerville.. Once the Dumbarton gets rebuilt, again far less cost than the monster extension around or through Livermore, then an ACE train could swap riders at Centreville w/ Cap Corridor trains to SJ and head over to Redwood City, offering transfer to the Caltrain EMUs for the final leg. As with any truly useful network of routes, few riders will use any of these trains end to end but the multiple options will be highly useful. The monies saved by not building unneeded BART mileage can finance Shinn St Station, the Dumbarton Bridge rehab, and more rolling stock.--there should be surplus midlife diesels from Caltrain and perhaps coaches as well if they get started soon.
And, of course, I hope in the few decades I have left, to see catenary from SJ clear to Sacto.