Butler,

The wye at Dozier is the product of the relocation of the Sacramento Northern on account of the runway expansion of Travis AFB in 1949-ish (I believe, formerly called the Fairfield-Suisun Army Air Field). The original SN line ran from Creed to the other wye you described west of Gate Road, named "Cordero Junction", at the northwest corner of Travis Air Force Base, adjacent to Vanden High School, where the SN overflew the Southern Pacific on a girder bridge (taken down in the 2000-ish timeframe). To the northwest of Cordero Junction is Vacaville Junction, where the SN's Willotta Branch and Vacaville Branch met and formally connected to the Sacramento Northern's south end.

The wye at Cordero was augmented during the above relocation with a connection to the Southern Pacific at "Cannon", near the intersection of Vanden Road and Cannon Road. The SN local out of Sacramento would later use trackage rights over the SP to Cannon, use the two wyes at Cordero Junction and the flyover, and proceed up the Vacaville Branch to switch the old onion plant on Davis Street.

Hopefully that's not too muddy and answers a few questions.