I would expect Amtrak to move Chargers for the Midwest from Sacramento to Chicago on the California Zephyr -- it wouldn't really make sense to do it any other way, would it? It's even simpler than the Sprinter moves: the Chargers can move directly into the Amtrak Chicago yards from where they will be deployed. I'd expect the Pacific NW and Pacific Surfliner Chargers to move on the Coast Starlight, as well.
AAF seems much more likely to move their locomotives by freight rather than Amtrak, unless Amtrak makes them a great offer; Amtrak would be a convoluted routing for them (Sacramento-Chicago-DC-Jacksonville, I guess). I suppose AAF might move their passenger cars by Amtrak, but it still seems like a freight routing might be better for them.