Just to update on this. I did board at South Station with a Back Bay ticket, and was able to board the train without any problem. As others stated, there was nobody checking tickets at the station. I walked all the way forward to the car behind the quiet car, which was basically empty when we boarded, but got more full after Back Bay.
However, on the train, they did "attempt" to scan tickets before we got to Back Bay. I say attempt, because the conductor had problems with her scanner. After we left Back Bay, it was working fine. Not sure what would have happened if they got to me before we got to Back Bay.