That quote you provided is boilerplate language inserted, in some form, in most if not all ICC and STB abandonment decisions. Precise language varied over the years depending on requirements of then-current trails legislation and court decisions. It preserves the Feds' rights if federal land was originally used for all or part of the r/w. It doesn't mean there *is* federal land in the r/w absent other information about how SP got and held title, which could be different for various parts of the line. I suspect they started doing that because the Feds did indeed lose rights to put trails on some rail lines that were abandoned before that clause became standard - the land reverted to surrounding owners even though they got their land from the feds after the rail line went in. There were a couple of significant court cases about that, most recently only a few years ago. As with most legal things, it comes down to details.

Most of the central Bay Area was held in ranchos long before statehood, which were recognized as private (not federal) landholdings when California became part of the U.S. I suspect that there is in fact little if any formerly federal land in the r/w, and that Alameda Co. is legitimately SP's successor in most if not all of it. A serious title search would be needed to be sure, which the county probably (hopefully) did before taking over, but it makes sense given the history of land ownership there.

And in any case, NCRy appears from everything seen in this thread to be simply the county's tenant, and as such can be evicted if something better comes along.