One, this equipment costs a lot of money. While one always does need to have some spares sitting around for bad ordered cars, one doesn't want to be paying off a loan on a car that ends up seeing only 15 to 20 runs a year. That's hardly productive.
Sure, but how accurately can Amtrak predict how big its fleet should be? Demand keeps growing, even without adding routes, and there's desire to add more routes, and multi-year lead times on cars that Amtrak can't cost effictively order one at a time. If Amtrak's goal were to buy enough cars so that the least frequently used cars saw 15 to 20 runs per year, I suspect what would actually happen is either that they'd have a bunch of cars that did fewer than 5 runs per year, or else they'd find that every car saw at least 100 runs per year, and it would be impossible to predict in advance which would happen.
(I'm also assuming for the sake of argument that cars would be sorted in some order, and used youngest-car-first or something; it's quite possible that in practice the non-peak trips would be spread out over the whole fleet such that you'd have 100 cars that each get 100 trips a year fewer than they could have been used for had Amtrak sold more tickets.)
But if Amtrak were going to replace all the Amfleet cars for non-peak use, would it make sense to keep the Amfleet coaches around for extra cars during peak times? I gather they haven't been too agressive about scrapping some of the other older equipment. Amtrak wouldn't be paying interest on the Amfleet cars at that point if the question is whether to scrap them or to keep them for 20 runs a year, but there probably are some maintenance costs that relate more to the number of calendar days that pass than the number of miles of track covered.
Third, you do add the sleeper because the existing ones sell out. Now you only sell one more room in the newly added sleeper, what do you do? Do you cancel that one reservation angering that person? Or do you run an empty car with one attendant for one passenger?
While this is not an entirely trivial problem, I think it's solvable.
Amtrak could reserve the right to change room numbers that have been assigned, and could call passengers looking for one who's willing to change the date of their travel in exchange for a voucher good for future Amtrak travel worth half (or something, I'm sure there's some manager who would would figure out what the minimum voucher value needed to actually find a willing passenger) of the accomodation charge, and then the passenger who was going to have a car to themselves could get whichever room was freed up.
(The other complication there is that if the one room that did sell in the last car is one of the bigger types, you may find that the people who buy those rooms are less easily persuaded by a small financial savings, given that they were able to afford the larger room in the first place. But if the reservation system only guarentees the smallest room at that point, that might still work out.)
Or adding the sleeper could be done only at times well in advance of the trip when Amtrak can be reasonably sure it will sell out.
Four, you do add the extra car of whatever type to the train. Now the car is someplace else and you don't have the passenger load needed to send it back to where it should be held. You now have to waste money dead heading it back.
I'm curious, does the Auto Train typically have the same load going in both directions all year round?
The other question is what Amtrak's purpose is.
If its purpose is to make a profit, then it obviously should only carry 2/3 (or much less, probably) of the passengers who wish to travel in the circumstances that happen to be most profitable for Amtrak. But that's obviously not its sole purpose, because most or all of its routes would be gone if profitability were Amtrak's sole purpose.
The reason we fund Amtrak must be that we believe that providing affordable train service to people who want to travel somehow benefits our country. Perhaps making Boston <-> NYC and NYC <-> Washington, DC travel easier for business travelers is good for economy. Or whatever. But whatever the argument is for subsidizing Amtrak, it's possible tha making passenger travel affordable and accessible to Americans includes those Americans who happen to want to make last minute reservations on peak volume trains.