Why? Because no only do you have all that runoff from the Sacramento River diverted through the Yolo Bypass (the Bypass ends northwest of Rio Vista, you also have runoff from the roaring Putah Creek, especially with the water level higher than the bell-mouth spillway at Monticello Dam, resulting in a lot more water going down Putah Creek.
That means every Sacramento-San Joaquin Delta island from Rio Vista and downstream are under threat, the cities of Antioch, Pittsburgh, and Martinez are under threat, the oil refineries east and west of Carquinez Strait are under threat, everything else along the shores of San Pablo Bay are under threat.
Your analysis is correct, unless there is a levee break further upstream on the San Joaquin or Sacramento rivers. If one of those breaks on a major river moving 250,000 - 350,000CFS, that will get a lot of people wet.
Of course their will be minor flooding at the base of every gully in the foothills, and the Consumes will flood I5 as usual.
But it’s time to worry about the big rivers now.