It's more about the fact you can run a non-passenger movement whenever, as long as it is not an Employee train (moving crew(s) from one place to another). Since it is now a scheduled move, it has to be slotted accordingly. The crew will now be on duty roughly an hour longer than they were when it was a deadhead train.
It will be interesting to see if the fine residents from the East End utilize this, though. It is quite obvious that people flock to the east end, but there are people trying to get the heck out of there, especially younger people wanting to go into the NYC nightlife. I think it will be well served, but the question will be: can a two car, sometimes one car train, handle things if it actually proves successful? I personally think the public timetable times are too long to maximize it's potential. We shall see, though.