Their agreements (leases) entitle them to certain things, most of which are beyond my knowledge, but I'm positive that the track owners control the traffic on those tracks. The owners also need to maintain those tracks to a higher degree per FRA regs for passenger trains. Passenger trains typically run at higher speeds than freight, so the tracks must meet the speed ratings of the passenger lines and weight ratings for freight (as well siting distances, crossing, etc. for both).
When working on the tracks, the owners provide track protection, and therefore any train on that line must yield when required. Owners can manipulate their own schedules to get around the work and based upon the cost of those delays, where as daily scheduled passenger trains simply get delayed unless there are penalties (typically from local commuter lines).
We worked at night on the Hudson line to avoid delaying the commuter trains. Garbage at night was delayed. On the Selkirk line, we worked during the day, delaying the Amtrak passenger trains, and avoiding any delay to freight.
All about the $$$$