Also remember, liquid shrinks and expands with temperature change. The fuel tanks on our trucks are only allowed to be filled to 90% capacity at any time. A filler tube extends just inside the tank to prevent it from being over filled. I have spoken with tank truck drivers about this and they are not able to fill the tank all the way either, and the liquid weight also determines what the haul-able max capacity of the truck is.
Im not sure what the standard for loading tank cars is or what it "was back in the day." Id bet it is a similar practice and has been in play for a long time, especially for the NG where there could be a large temperature swing on any day and across the multiple days a trip may take.
90% of 6000 gal would be 5400 gal. If you base it upon Rich's math and the volume of a tank car is 6700 gallons, the 6000 gal cap is about right...
Casey