1.) USGS survey data confirms that at one point the Pennsylvania Railroad extension to their Exchange Place terminal along the harbor had a connection on the lower level to what is still called today, the "National Docks Branch". The history and deals made between the railroads in the early 20th century required a plethora of switches and connections to the freight docks mostly controlled by the Lehigh valley RR. Just south of the Communipaw Terminal. In fact, this at one point was just a branch, the tunnel portion going south in this direction was added later. Link to the USGS maps website. https://ngmdb.usgs.gov/topoview/viewer/#15/40.7255/-74.0614 

2.) I have been to the site while railfanning in the area. The ROW is still intact. Fences are there to keep pedestrians away from the in-use lines. Typically, on mothballed or disused ROWs. 