Hi Dr. Z.,
Thanks for your reply. Here's my reply:

1) USGS Map not drawn correct: I took a second look and I agree it's got a lot of errors. They seemed to have combined the Santa Fe tracks with the Key mains in the area around the station. Over by the wye they have the wye and tail track correct. But at Hollis St. they sort of falter, lose track, and merge those wye track into the key track while ignoring a third Santa Fe track that lay between the wye track and the Key mains. Good studying of the map!

2) USGS Map is dated 1959 with photorevision 1980(in purple). You can find that here. Look for the West Oakland quad: [digicoll.lib.berkeley.edu]

2) Tracks in Key underpass: I looked more closely and in 1965, as you report, the underpass had been converted to vehicular use. On the west end of the underpass you can see a fence where the rails would have headed west. Anyways, here's a link to the photo: [mil.library.ucsb.edu]

3) Link to 1931 photo (great detail in this one) is here: [mil.library.ucsb.edu]

Thanks for your help!