At the down line stations the train doesn't sit at the station for more than a minute or two, unless there is a problem. Even then if there is a problem, the train is still sitting there with its operating crew onboard and most likely even its passengers.

At Boston South Station, since it is an origination point, trains are often backed into the station an hour or more before departure and then sometimes left unattended for a while. So they don't want people just wandering around down there and potentially taking the train for a ride, or attempting some form of sabotage. And since each platform can serve two trains, they are trying to protect both the train you are boarding and the possible unoccupied train. They also want to make sure that you are boarding the correct train too, one reason that they check tickets in NYP. You'd be surprised at the high number of people who board the wrong train at Penn.

Down line stations don't typically have more than one train in the station at a time, especially going in the same direction. So it tends to be less confusing, although even then people still get it wrong.

Additionally even during boarding there can be occasions where the engineer or a conductor has to leave a vital area unattended to go and fix something, so again the check tickets to ensure that you belong on that train and aren't looking for an opening.