First, I don't understand "...regardless of what the rules say." The rules say get out of their way, you're doing the right thing, although it's simply unnecessary hereabouts. I think you may have it backwards.... and will continue to do so regardless of what the rules say. It seems to me, though, that most ferries here are operating in a traffic lane and are therefore the stand on vessel. This would include the Oakland-Alameda estuary and the route the ferries take from there to SF, as well as the Alcatraz ferry.
Re traffic "zones", John, that's simply not true. The traffic lanes you describe are for the BIG ships, not the ferries, including the estuary. The BIG guys look at the ferries as small craft! The Vallejo ferry actually leaves the channel when it turns the corner in San Pablo Bay going north and east and stays well south of the deep water shipping channel. It is a coincidence that they follow them, because most of the Bay is a shipping channel (almost!). The Alcatraz ferry CROSSES the eastern shipping lane (i.e., south of Alcatraz) at 90 degrees! so it can't be "using it."
I've found the Alcatraz and harbor tour ferry skippers (who go under the Gate and turn around) among the most courteous, although I haven't found one who ever wasn't in 35 years sailing here. These two routes are right through the busiest racing venues of the Bay: tacking up the Cityfront. Those ferry guys are better at dodgin' racing sailboats than are most laid-back cruisers on sailboats!
The Vallejo ferry skippers are great since they're moving so quickly, but make their turns to make it obvious they'll pass you, and usually astern of you, too. They leave a dual wake: big rollers and short chop, which arrive at different times! Fun and games.
The Oakland ferry drops south of the shipping channel right at Est 8 (red) and uses A-B span, not D-E. Definitively out of the shipping channel.
Rather than continue to dodge them, John, I recommend you continue to be prudent, but start looking around and see how nice they really are. Then, when you go sailing somewhere else, forget everything you ever learned here!