> Although legally passenger trains are now supposed to have right of way over freight trains, in practice that’s just not the case

Amtrak has right-of-way over freight trains if they are claiming their pre-allocated rail time slot. If a freight train is already on the track at its own scheduled time, it's going to take it, regardless of scheduling priority.

Unfortunately, Amtrak is independently dysfunctional (I'm sorry, it's true, it's led by people who don't know anything about trains) and is rarely on time even independent of rail congestion, so they show up at times they weren't scheduled, and the lateness compounds as they get further delayed by congestion.