Back in the 70's BRILL Interlocking (armstrong for many years, and I think right up to the end, named for the streetcar manufacturer; a wall of one of their buildings still stands nearby on the west side of the tracks) was where the four tracks became two double-track lines, the easternmost becoming freight tracks leading to the High Line and the westernmost becoming passenger tracks as far as ARSENAL Interlocking (named for an arsenal that was there during the Civil War), where the tracks to the Lower Level went straight and trains for the Upper Level crossed over to the Octoraro Branch (coming in from Media and heading for the Upper level); so it's easy to imagine that the operator at ARSENAL thought the train for the Lower Level was ahead of Amtrak instead of behind it. Today, BRILL is no more (straight-railed, as they say), and ARSENAL on Amtrak is no longer an interlocking but simply automatic signals. Sometime during the 1970's -- certainly after 1971 -- PHIL Interlocking was built, bit by bit, north of ARSENAL while a full schedule of Amtrak and SEPTA trains was being operated (sort of like a restaurant installing a new kitchen floor while preparing and serving a full lunch and dinner menu every day); it separates the flow from essentially Amtrak on the inside tracks and SEPTA on the outside to (from east to west) Track 1, NS to the High Line; 2 and 3, Amtrak to and from Lower Level; 4 and 5, SEPTA to and from Upper Level. The Airport Line is a single track crossing overhead from east to west just south of PHIL and becomes track 5 at PHIL. Tracks 4 and 5 swing over to join the double-track line from Media at ARSENAL, still a Controlled Point on SEPTA.
Yes, you have it right, except that the timetable direction from Washington to Zoo is northbound; Zoo to New York is eastbound, and Zoo to Harrisburg is westbound. As it was in the beginning on the PRR, and apparently ever shall be, world without end ...