The main trunk lines are in Long Island are about 3-4 miles apart. Northwest of around Cupertino or so, the mountains edge too close to the bay shoreline for you to make a second trunk line viable. Your best bet would be plonking a line around about 85, but the right-of-way doesn't exist to actually hook that line up to the existing line in any useful way.

And outside of that, basically everything you'd consider plonking another path already exists with some service: BART runs up the east shore of the bay, as it does west of San Bruno Mountain. You have two mountain crossings covered by BART and one by ACE. The main missing things are curving BART back into San Jose and reactivating the Dumbarton Bridge.

Your last sentence was going to be my reply. The peninsula is really linear along 101 / the historic el Camino. There really isn’t anything to connect to.

LIRR still had to do plenty of tunneling to build the East Side Access station though. Still, it opened in 2023! NYC is also still building the second avenue subway --- slowly, haltingly, and at near-ruinous expense, but it's actually a real expansion to the network is actually happening. By US standards, that's a miracle.