When CSX's faulty track work lead to the derailment of Amtrak's Auto Train a few years back, the only money that CSX paid out was to fix the tracks that it didn't fix right in the first place, along with the added damage caused by the derailment. Amtrak paid every claim, and paid to fix it's own equipment.
This is a very long-standing arrangement whose nature predated Amtrak by probably a century or more. It is called by some the "but for" clause. It means that but for your presence the event would not have happened. It is more or less standard in any trackage rights agreement. That is, anything that happens to a train that is running on a track owned by someone else, in other words as the the trackage rights tenant, is the responsibility of the tenant, not the host railroad. Except in the northeast and a few other places, Amtrak is the tenant, not the host.
It is not some special and unique "screw Amtrak" clause. It is the normal track rights host / tenant arrangement. The same would be true for, using as an exampe, a NS train crossing accident or derailment between Wauhatchie (Chattanooga) and Stevenson, Alabama. It is a NS train on a CSX track. CSX fixes the track, NS fixes the train. I pick this as an example because it is one of the oldest trackage rights arrangements out there, going back to at least 1850.