I'm not sure what that lesson is, though. Obviously meeting commitments is a big thing, and Amtrak should find a way to do that whenever possible. But Amtrak is also hamstrung by a couple things that FedEx isn't, the sum of which makes Amtrak late (and thus Amtrak can't "learn" how to fix these issues by looking at FedEx):
1. Amtrak, for the most part, must use train travel along the route. They do have the option to use buses, but many customers will be displeased with that option and demand a partial or full refund simply because they were transported by bus (even if they make it to their destination on time.) With FedEx, the package can take any transportation option (rail, road, air, and whatever other options that I have missed) and as long as it makes the deadline and arrives in the same condition it was shipped in, no one cares what method of transportation was used.
2. Building off of 1, Amtrak is not only limited to rail travel, it's limited to rail travel on a specific route, which in the case of the Empire Builder the owner is basically telling Amtrak that it can't run on-time and that it will be 4-6 hours late most days. Amtrak can't use a different route either, so they basically have the option to either just grin and bear it, drop the route, or lengthening the schedule (if the owner of the rails allows it.) With the latter option, Amtrak also has to make sure that they have some sort of clause to go back to the original time once the delays end unless they want to have the lengthened schedule indefinitely.
3. Amtrak, if they arrive to an intermediate point on their route early, cannot leave until the time they're scheduled to leave. FedEx can deliver a package earlier than promised and not have to stay at the customer's location until the committed time before they leave. Amtrak doesn't have that luxury.