This project is being driven by Cuomo. He couldn't care less about NJ-anything.
But there are aspects of both the current Penn layout and the planned Gateway program that relegate NJT to the southern platforms, and the eastern section of the station. So any westward expansion (Farley / Moynihan) was never going to include NJT.
When they build all of Gateway, it will ideally include Penn Station South, which will expand the whole station one block south, including new platforms. That will address NJT capacity at Penn.