For example:
* Penn Station Dwells are not limited by passenger movement at doors. It’s not a metro, go and watch trains being loaded.
* Escalators constrain the rate at which people can actually reach the platforms
* These escalators need to switch direction when a train arrives, meaning multiple arrivals and departures are not simultaneously supported.
* The tracks do not support all operators and the station design divides Amtrak from LIRR
* Some tracks do not support full train lengths
* Not all tracks in the station are through tracks
* Trains are terminating at NYP which requires a longer process of ensuring no passengers are still on on board before leaving for the yard.
* It’s not only the north and east river tunnels, there is an entrance from the Empire line for Amtrak and separate paths to the WSSY for LIRR, not to mention train storage within Penn in the ACDE yards.
* Engineers walk the entire length of the train when a trip reverses direction. This takes a long time. The OP mentions through-running solution, but doesn’t point out the problems with it, namely incompatible equipment and giving an entirely different agency access to your multimillion dollar trains.
I could go on and on.