But they do. The same NH trains that run on the AC Catenary also operate off the DC third rail when they join the old New York Central Harlem line as Mount Vernon West. It's all 3rd rail DC the rest of the way. Unless it has to do with Amtrack requiring the AC Cat system as they do run along the NH line, I think... However doesn't Amtrack also run along the Hudson Line which is also a DC 3rd rail system ?
Outside of the NYC subway system my knowledge of railroad routes is limited. My interest in trains is limited to subways.