This concerns the end of the Q post.
While no sauce, I had worked with BNSF on their transcon and learned a few things. Every railroad has its own police force with jurisdiction to anywhere the track goes, and some feet past the easement.
Intermodal facilities, while not at the shore, have a direct line from ships to trains, and these facilities are very large, with TSA clearence required.
On the train runs from L.A. and SF, the trains pass through NM. Internally it is seen as a theft prone area, with whole containers being emptied in short order anytime a train is stopped for traffic.
From the west coast to chicago, no inspection of the contents is performed, and any claims happens after arrival at the final destination.
The intermodal trains are considered high priority and are the fastest of all the trains on the network, getting to chicago in two days without the train manifest changing.