From a legal perspective, you don’t need Amtrak’s permission to take pictures of somewhere that they have no reasonable expectation of privacy.
They permit photography on their trains (within the above quoted guidelines), and I don’t need a random stranger’s permission to take their picture in the common area of a train.
As you and I both correctly note, none of that is worth a bit when someone takes offense at your photography and takes a swing at you, damaging your gear or worse.
But that’s a personal decision for the OP to take. Everyone takes risks in life, it’s up to them if they want to take this particular one. For whatever little it’s worth, the law and Amtrak’s policy are on their side.