Right, but there's nothing preventing sending the freight service on the LIRR main line tunnels (other than it possibly getting in the way of passenger service,

Right, but there's nothing preventing sending the freight service on the LIRR main line tunnels (other than it possibly getting in the way of passenger service, which can be avoided by doing it in the middle of the night). These freight and passenger lines weren't built separately. They were literally part of the same railroad. Though I do admit the shortline barge is still a reasonable option to avoid the scheduling and bureaucratic complications of the "Penn-freight" route.