Originally Posted by
Enkidoh
I took the name to be more metaphorical of it's nature as a military supply line - you know, the military term 'ghost' referring to something that is clandestine/secretive. It's not a real ghost train, just a Garlean black-ops railway that moves supplies and equipment between the two Castri secretively (hence why during Operation Archon the line was blockaded by the Order of the Twin Adder - if they didn't Castum Centri would have easily been able to reinforce Castrum Meridanium right when we were infiltrating the place and the Alliance would have lost the battle).
So yeah, it's just a reference to it's secretive military nature and is not FFVI's actual ghost train I'm sorry to say.