I don't know, KarlJ - everything I've ever heard about it and everything I can find on the internet make it seem like a pretty firm Visa and Mastercard policy. Why would they make an exception for Amtrak? Here's another link to a credit card info FAQ.
http://www.creditinfocenter.com/cards/c ... #Question5
By the way, swiping is NOT required by credit card companies. There used to be (maybe still are) some small businesses that didn't even imprint - they just filled out the carbon form by hand. All Visa and MC care about is properly recording the name and number and getting the cardholder to sign. If Amtrak doesn't swipe or imprint on board, how do they record the transaction?
Note also that pre-approval is for the protection of merchants, but is not required by the card companies. If you as a merchant don't pre-approve, or get approval at the time of the transaction, you're taking a risk that the charge may not be approved when you submit it. But that's the merchant's problem, not Visa's or MC's.
If it's really true that Amtrak has a unique agreement with Visa and Mastercard that allows them to set a minimum purchase amount, maybe you could tell us how you know about it, and how Amtrak convinced the card companies to allow it.