> There's one facility to transfer garbage from trucks to trains in a marshy corner of SI

I am 99% sure there's another one in East Williamsburg because I've seen it with my own eyes.

edit: Oh you actually mentioned it

> No freight trains are allowed through the tunnels leading to Penn, nor GCT.

IIRC the Pennsylvania Railroad experimented with this during World War 2, running a test freight train through the Hudson tubes.

I think it became disconnected and immobilized.