No one will be booked into the unused beds in your room. The room(ette) is yours for the duration of the trip.
Meals in the diner however, have always been community seating. If you have less than four in your party, you will likely be seated with others. Meeting others over a meal is one of the many benefits of long distance rail travel. It's a pleasant reminder that before websites and email we were once social creatures capable of engaging conversation and debate without people being in 'our space' or offending one another.
Taking meals in your room is an alternative.