Ah, the Penn Station Grand Central connection with run through rises again. Another favorite boondoggle of starry eyed planners and dreamers who have never bothered to check their dreams against realities. Unfortunately they have apparently never bothered to run a single simulation, which would very quickly show that the traffic imbalance in rush hours between inbound and outbound will cause one to either run lots of empty trains long distances or gum up the works in the tunnels under Manhattan big time.
Wrong. I take it YOU have never bothered to run a properly calibrated simulation. The traffic is far more balanced than you think it is. Have you actually checked NJT schedules?
I see that Jishnu has chosen to bite his tongue Nathanael with regard to your post; so I'm going to speak briefly in his behalf. Jishnu is NJARP's liaison to NJT. The man lives & breathes NJT schedules. If he ran a simulation, I can assure you that he considered every aspect, every train, every switch in his simulation.
I also know for a fact that Jishnu has attended almost every meeting there has ever been on all the various plans & options for increased service into NYP, connecting tunnels to GCT, and even the now dead NJT plan for new tunnels to 34th Street. He's spoken personally with big whigs at these events and has I'm sure gotten some insider info that he's not at liberty to discuss publicly.
Since you mentioned flooding in NYC, let me put it this way; if NYC was about to flood and I needed to take just 1 NJT train out of 10 to get out of the city to save my life and I was given only 1 phone call, I'd be calling Jishnu to see which NJT train I should get on. Yes, that's a bit of a contrived set of circumstances. But the point is, if I really need to know something about NJT, Jishnu is the guy I'm calling!