When they add that many cars, the rear of the train hangs out into the street at Jack London; adding the cars in the yard cuts down on the time the train is in the station. (Incidentally, that's why the Zephyr stopped running to/from Jack London several years ago--when they added the boxcars/reefers to the consist, the Zephyr wouldn't fit between the signals and street crossings at each end of the station. For whatever reason, they kept Emeryville as the terminal even after the freight cars went away.)

In the Oakland coachyard, track #8 is specifically inspected to allow passenger-carrying trains to enter the yard. The other tracks are "excepted" so can't be used for a train with passengers on board. Actually, all the track in the place is built like a brick s**thouse and is fully capable of this use, but is not inspected per FRA rules.