Occasionally they will also be "reserving" these seats for expected large loads at stations downline. Trains serving Richmond's Staples Mills station will often have a car or two "closed" because they know that 80-120 passengers will be boarding there.
Makes it easier for everyone if you really think about it. And "yes" as much as we all "like" to spread out in two seats, your right about your ticket only entitling you to one seat.
As busy as Amtrak's Regionals seem to be lately, I really can't blame a conductor for trying to "herd" his/her passengers into selected cars.
What I don't like is when other cars are open, but they ONLY WANT passengers detraining at certain stops in those cars. Maybe the seat has a better window, (cleaner, better positioned, etc) or there is too much noise, or the AC/heat is bothering me......