So guess I'm old now, because I remember when this was put in as part of the big dig redesign of this area. The track (referred to as track 61) was intended to maintain freight rail access to the South Boston Waterfront. As far as I know there was never a revenue run down this track to the waterfront/docks since there are no active customers down there.
If you go to google earth you can see the tracks running down to the water. Follow Haul Road from the Convention Center to Drydock Ave and eventually to the docks.
Over the years there have been rumblings here and there about getting customers in this area online but honestly, I think this line is dead forever.
Wikipedia has a write up of the track here:
https://en.wikipedia.org/wiki/Track_61_(Boston)