What about California?. Especially for Commuter RRs. Its complicated there. example-- UP runs by the San Jose station and runs parallel to the Cal Train track for some distance,
Probably simpler than you think.
For Amtrak, pretty much nothing can run. It is BNSF from CP Soto to Fullerton Jct for the Surfliners and from CP Soto on for the SW Chief and UP north of CP Los Posas in Moorpark, so that let's out the Surfliners, the SW Chief and the Starlight. Up north, it is UP from CP Coast in Santa Clara on. So nothing can run, not the Capitol Corridor on UP, nor the San Joaquins on UP and BNSF.
With regard to commuters, Metrolink won't be able to run anything except the Ventura Line as far as Moorpark and the line out to Lancaster, as those are wholly SCRRA owned. They won't be able to run anything south or east as those lines have large sections on BNSF and UP. The Coasters will probably be okay as that line is all NCTD owned.
Up north, CalTrain can run SF-San Jose as that is all PJPB owned. They can't run to Gilroy as that is UP owned. ACE is all on UP except the last little bit into San Jose. I don't think ACE crews are unionized, so don't have to respect picket lines, but they have to have UP dispatching.
The dominant factor is likely ownership and dispatching. I doubt trackage rights will be a factor. The freight railroads have trackage rights over pretty much every inch of commuter agency owned rail in California.