This is patently false - Amtrak has the right of way by law.
The reality is:
1. if the siding is only 1km long - the Amtrak train is taking the siding as the freight train will not fit on it.
2. if the dispatcher decides the freight train goes ahead of Amtrak -- there is no lawyer around to argue the point.
3. if there is a long section of single tracking, with freight backed up the opposite direction, the dispatcher allows the all the same direction freights to move. ( 2+ hour delays when that happens )
4. If there is enough of a delay and a freight train crew in front goes outlaw - then that train stops until a replacement crew is brought in... which usually results in the Amtrak crew going outlaw as well.
It has gotten a lot, lot better and the scenery is beautiful - but please don't kid yourself about the realities on the ground. Amtrak has to stay in the good graces of the railroad companies especially with a hostile congress.
What qualifies as commuter rail? I think most of Amtrak's cross-country tracks would probably not be considered intercity or commuter lines.
The real issue is that often operationally, a passenger train has to stop for a freight train. If you have a 1000' siding that you have to have a 6 car passenger train pass a 30 car freight train at, the passenger train is going to have to stop for the freight train. That doesn't even take into consideration other factors like how freight dispatchers don't like to stop hazmat/"hot" trains for safety reasons.