There would have been 6 to 8 OBS crew on that train, excluding the SCA who has room 1 in the 30 car, depending on whether or not there was a cooks helper and/or a second diner service attendant or not. That leaves 8 to 10 roomettes, ignoring the mid-car Sacred Territory boundary.
The OP was automatically re-accommodated, although in coach. A cancellation is different than re-accommodation, I know, both have happened to me. They generally do not cancel then re-accommodate, they do one or the other. Yeah, if they cancel you these days you have to call to get it straightened away and get back on a train, and it is best to call early, but as I said, it is either one or the other. Your premise is the roomette passengers in the 31 car actually got first crack at the sleeper before a bedroom passenger in the re-accommodation list. Since the train was not running a transdorm before, there were likely no passengers at all manifested in the "40" when the swap took place. And there would have been roomettes enough to accommodate all of the bedroom passengers and then some, with at least 8 roomettes in the transdorm not needed by the crew and 5 bedrooms in the 31. So, yes, there may have been an IT problem and did like for like (roomette to roomette) before they did the much more expensive bedrooms, which I would consider a pretty serious oversight, but Amtrak IT is a clown car so I can readily believe that. They also could have just limited the number of revenue pax in transdorm to the traditional 4 roomettes and the OP drew the short straw for the 5th bedroom. Ignoring the fact that there are 8 roomettes in the rear end of the car, and even if there were 10 crew roomettes needed, with 2 required in the aft end, there still would have been 6 available. Unless Amtrak prevents the horror of a crew member being booked next door to a revenue passenger.
Maximum coach attendent staffing these days is one per 1 1/2 Superliner coaches. The T&E crew generally handles whatever needs to be done on the train side for the baggage car.