The Regional Plan Association proposal to create a new transit hub at Sunnyside Yards and a unified Metro New York commuter rail system would never work.
The idea of Long Island Rail Road and New Jersey Transit trains providing passenger service in portions of each other's service territory has been periodically proposed for decades. It has never been implemented for good reasons.
There is no way NJ Transit and LIRR can convert Penn Station to an intermediate stop. How could you maintain existing service and convert Penn Station over years at a cost of billions to implement this service change?
Most LIRR and NJ Transit equipment is not interchangeable and can not run on each other's track as they obtain power from different sources. The same would be true with future Metro North service to Penn Station.
You also have to deal with different unions along with accompanying union work rules, employee seniority and contracts. There are also different fare structures and fare collection systems.
It would also cost billions to purchase compatible equipment and modify power and signal systems.