I havnt looked in to the auto train since they changed it but yes, i believe we must pay our fare as well as NO chance to upgrade to sleeper accommodations even if they are empty. Amtrak would often stick first come first served employees traveling on pass in to open sleepers on the auto train to give coach passengers some "breathing room" as coach can fill up quick. We have to pay for the seat, the car, and the food.
The biz class travel is no longer allowed. Acelas we are no longer allowed to do within an hour of travel and zero first class. We used to be able to do first class for $30 and biz for 5 on regional or acelas. They will let a biz class go half empty before they allow employees to take a ticket in one.
And my statement of riding in coach for free on any train, i mean any train thats on a blue day off corridor. Corridor rides we can pretty much always get on, but are not guaranteed a seat. There is no such thing as a standby for amtrak pass rider employees. We either book a seat/accommodation or we do not ride that train unless again, corridor trains do not require a booking to ride and pretty much works as first come first served. Now however! if you are an employee scheduled to deadhead to a trip or from a trip as part of your tour of duty, and you are assigned to that train to deadhead, then technically you should have a coach seat as you would be on the manifest. But even at that, on some very busy trains they may not have anything available due to overbooking.
No good deed goes unpunished.