Separating AMTK from NJT/LIRR/NYCTA is not a good idea and the Farley building is too far west of 7th Avenue and subway connections to be attractive as a primary station facility - put "The Garden" in there and forget it. Further, the proposal ignores the very valuable air rights above the station.
During my years in NYC, I never really figured out the existing maze. A unified station plan with simplified passenger access between carriers is essential. With existing trackage and platforms being at the same level, I suggest revisiting the original inspiration for the Penn Station, the "Gare d'Orsay":
Money being no object, an open grid pattern of multiple elevated walkways, crossing all tracks and providing access to all platforms, connected by several walkways running parallel to the tracks for the entire length of the platform area, would solve the problems discussed - including catenary support. A control point, waiting room, ticket sales and baggage handling area at the 7th Avenue end of the station would tie the entire system together. Proper signage would allow passengers to SEE where they need to go and easily determine the most direct path to that location; the lower level could be dedicated to baggage and mail handling.
An atrium above the walkways would provide the desired sense of openness. Two intersecting elevated walkways at street level, above the passenger walkways, would allow easy, protected access from surrounding roadways to the controlled station entry point. Finally, an office building above the atrium, with adequate access points, would utilize the air rights, provide revenue and have the added benefit to occupants of ready access to transportation.
Should there be a need for additional tracks and platforms associated with new tunnels, a simple southward expansion of the station, using the same pattern and system of interconnected walkways, would resolve that issue.
Attempting to adapt present site architecture to fit today's and tomorrow's wants and needs is like trying to fit 40 lbs. of "stuff" into a 10 lb. box, you just wind up with a bigger and, ultimately, more expensive mess. The City and State of New York seem to find adequate funds to finance all their other zillion dollar boondoggles, why not one more that might actually benefit the people of the metro area?