Nobody who stays at a roadside hotel which offers free breakfast - as most chains do - would argue that the breakfast was pre-paid as opposed to an amenity included with the room. So why do we need to make such a distinction with Amtrak?
For hotels, there is competition. One hotel might charge $89. So the hotel across the street also charges $89, and tosses in a breakfast to sweeten the deal.
Is that breakfast free, or pre-paid?
I make the distinction between an advertised "free" breakfast and one that comes with the room. If it's really free, I could walk into the hotel and eat breakfast without staying there. The breakfast is included in the price of the room, just as meals in the dining car are included in the price of the room (except on the Silver Star).
Americans like to see the word free, but an advertisement saying something is free does not make it free. The meal, whether in a hotel or on Amtrak, is included in some other price.
Since it is included, there is no refund if the customer (not guest, even though businesses like to say guest just like businesses like to say free) chooses not to partake.
When traveling by train, I sometimes stay at hotels that allow customers to park a vehicle. Since I have no vehicle, I don't park one. I get no refund or discount. Nonetheless, parking is not free; it is included in the price of the room. If parking were free, someone could park a vehicle there while taking a train trip.
In short, it is a distinction with a difference. Included is not the same as free.