I was just typing in an answer when Bob beat me to it. As mentioned, while the website quotes you a single price, you actually pay one price for the room and the equivalent of coach fares for each passenger. Try a sample purchase with two and three people and you can see the difference.
Knowing how weird Amtrak can be, there is a slight danger that changing the reservation might increase the "bucket" price for the underlying room. I hope not, but it wouldn't hurt to ask. If I were you, I'd call the standard number and ask, and then call the Amtrak Guest Rewards number (1-800-307-5000) and ask again. The AGR folks tend to be a bit more knowledgeable and friendly. You don't have to be on an AGR ticket or even a member to use that number, although of course you should have an AGR number and use it.
If everyone agrees that you can drop a passenger, get a refund of the individual fare, and not reset the room rate, go for it. You're better off going for the three at first and then dropping one later. I don't know about Amtrak, but cruise lines sometimes reach the maximum passenger count and won't let you add someone later even if the cabin has the beds for it.
