The big issue with ESA loading gauge is the east river double deck tunnel, the top level of which the NYC subway F train uses. If the tunnel were not in use on the top level they might be able to modify it, but that as they say is the way it is. Not sure how many of you have been through that tunnel, but you can tell there's space below by how it sounds, especially comparing it to how it sounds though manhattan. and in fact if you are nerdy about rails enough you can go to roosevelt island station and hear the equipment moving around in the lower level through the station. Will be interesting once revenue train traffic commences, hearing a train coming through but not seeing it..... :D
Yes, the connecting railway route/hell gate line etc important, but if NYP dead ended at 7th or 6th ave there wouldn't even be the chance of constructing such a link, not without serious property/zoning/NIMBY issues at the least... Thankfully PRR had some future-proofing geniuses, and we have them to thank for the modern NEC and how it connects the northeast megalopolis. GCT now reduced to a commuter terminal only.
Next stop the square, journal square station next!