Similar to going farther west in Sonoma and Marin Cos to avoid car traffic/increase scenic beauty on what will be the return on your counterclockwise loop (if I understand correctly your plans) I find that going farther east in the east bay, south of the bridge crossing avoids the blah, the blech, and the particularly increased incidences of bad car driving of the southern approach to the Carquinez/Alfred Zampa Memorial Bridge. I like that bike line on the bridge itself a ton,* as I do the roadway over the two miles just south of it — but the rest of the way between there and The Bay Trail Bikeway along the water feel like “junk miles” one puts up with for the “real treats” on other parts of a long route.
I feel the same way (Blech, blah, hypervigilence to deal with motor more vehicle operators who dislike cyclists) about riding through Vallejo and American Canyon. It could be that there are bike paths or a collection of local roads to take instead of the main routes through those towns. If so, I would love to learn what and where! It adds plenty of miles and elevation, both, to go the long way ‘round from, say, Lafayette to Martinez and then over the Bridge there to Benicia from whence one can take Lopes and Red Top to Hwy 12. Hwy 12 has a wide shoulder with nice hills to the right, but it’s not pleasant to ride in the afternoon when people are impatient to get home or wherever they’re in a hurry to go.
* this is my fave Bay Area bridge to cross at all hours; the GGB is equally wonderful between 5pm and 9am, but so crowded 9am-5pm, the majestic experience of biking the icon that I’m lucky to call “my hometown span” then turns into a “pedestrian” and pragmatic necessity to access better things.
If you don't mind longer, you could go further north from Napa and head over to Glen Ellen from Oakville Grade, or head over to Santa Rosa from St. Helena or Calistoga. Once in Santa Rosa there's a trail to Sebastopol or you can do roads, then you can head through Valley Ford and Tomales and down 1 all the way?