I've sailed this area for years. This guy went out during daylight, the sea was good, as was visibility. Even a collision, however unlikely, would have left some remnant of the boat. BTW, the Farallons are not at all that far from the SF bay inlet, so the search area was fairly well designated. I've never seen a floating container in this area.
Not finding the boat indicates he took the boat elsewhere.
I'm also a local, long time sailor. There's been quite a few instances of big ships ramming small craft and no debris remaining. I don't know what the visibility has been offshore but here in Alameda there has been periods of low visibility (read fog) over the last several days.
The area between the gate and the Farallons is a major shipping lane with ships coming from north, south and west. They don't always stay in the lanes and they don't always keep a good look out. I've had some close calls with the bigguns myself over the years, and that's standing a constant watch. A single hander can easily get distracted or become ill and not see what is coming right for him.
As to taking the boat somewhere else, there's only a few places places within a reasonable distance: Half Moon Bay or Drakes Bay. I imagine the CG has covered those bases.
Unless the guy got a total wild hair and decided to go off voyaging without telling anyone, he's on the bottom.