I think you'll be surprised at 2 things:

1) SMART will indeed get a good-sized ridership bump with the ferry connection. Not as big as it could be without the hike between the train and the terminal, but pretty good-sized. Without the bus transfer in San Rafael, more people will ride the train to the ferry than now take the bus shuttle.

(What remains to be seen is whether the ferry has enough surplus capacity to handle what the train brings to it.)

2) Neither BART nor MTC frankly care to spend the 10s of billion$ needed to extend BART to the North Bay; they have other uses for the money. Neither does the Marin Board of Supervisors. Neither does the SF Board of Supervisors, who would be less than happy about tearing up Geary for 10 years to do the job (among other things)