Maybe the pax could book the 2nd reservation with a middle initial, and not add the AGR# until right at departure time, so to the system they look less alike.

Also do you know anything about when and how this Amtrak conflicting reservation sweep procedure works? For instance does it run every night, or several times a day?

Since Amtrak does not readily allow same day changes, like Southwest, I could see pax on occaision might book more than 1 train, and then just refund the unused tickets or use the unused ticket value for later travel (like on Southwest). For instance your traveling NYP to WAS but you don't know wht time you actually want to or would be ready to leave NYP.

Also I wonder if Amtrak will ever be able to do standby like the airlines especially at bigger stations. Wonder too how high the no show factor is since at least in past you could get a refund or re-use the funds without penalty fee.