There’s a reason experts keep suggesting through-running. It’s a good idea that would deliver a lot of different benefits. The current setup is just not smart.
The obstacles are (mostly) not technical. It would not be difficult to get rolling stock that could run on both overhead and third-rail power. Although it would be “nice” to get the whole system on overhead, that’s probably never going to make financial sense.
If NJT currently needs bi-level trains for capacity, I’m not sure through-running would remove that need. Perhaps with through-running and four tubes under the Hudson, bi-levels might not be necessary anymore, but I have a hunch they’d still need them.
Of course, through-running would be a massive, massive project and the main obstacles are political.
Metro North has trains that can do so (M8’s). The biggest issue is that the New York Central decided to use under-running third rail when they electrified in the early 1900s while the LIRR and PRR use top-running third rail. This alone makes things complex since the M8 trains cannot switch from top to bottom running third rail on the fly although they do have the capability to run on the LIRR. Another problem is that the M8’s lack the required transformers for the PRR 25Hz electrification used in NJ and points south which would make the trains heavier or take up more space.
If the NJT really wanted to through-run into Long Island, they can simply run the ALP45DP’s on diesel once they’re out of the overhead catenary of Sunnyside yard. This is what Amtrak will do when they decide to run trains into Long Island.
Another option for the LIRR would be to extend third rail to Secaucus and build a storage yard nearby. The 3rd rail already runs to the entrance of the Hudson tubes to permit Amtrak’s dual mode P32AC-DM’s to run into Penn.
Thru-running makes no sense. It isn’t smart. It doesn’t benefit either constituent agency. No one at MTA or NJT is talking or thinking about thru-running. The End.
Through running could be as simple as running LIRR and Metro North Penn Access trains to Secaucus and NJ Transit to a new station in Sunnyside. A more robust through running setup would have Metro North running down the NEC, LIRR diesel dual modes running to Port Jervis and Spring Valley via a new Secaucus loop, and NJ Transit serving Port Washington via dual diesel dual modes and or Jamaica station.