The GG Transit semi-express commute buses now take about 2 hours from Santa Rosa to SF, without the ferry transfer, and with stops only along Santa Rosa Ave. and (when I took it some years ago) through Petaluma. Yes, they're subject to traffic, but most of Marin now has diamond lanes (only in spots when I rode it) so the schedule should be fairly reliable. Unfortunately, as with most fixed-route transit (including SMART), it runs between fixed endpoints on a fixed schedule, so when things change (e.g. jobs moving to East Bay) it's hard to change with that. Now if GGT or somebody else could set up a Larkspur-Berkeley or Oakland ferry run that might change the picture a bit.

I suspect SMART will be used more for Sonoma-Marin and intra-county commutes, by line and hourly staff (not the bosses), than for SF commuters. SF commuters, while an important flow, are probably not the driving force for N. Bay traffic any more.

BART at one point considered another transbay tube from SF to Marin. Made even less sense than running on the bridge. Ultimately, the costs plus Marin deciding they really didn't want to be THAT accessible killed the N. Bay leg.

Otherwise, I agree with your predictions.