This is a very odd and disgusting question: Where do train operaters "eliminate their waste"? Are there toilets on board locomotives or do they wait until they reach a planned stop along their route. If there are toilets on board locomotives, what about the days where steam locos ruled the rails.
These days retention toilets are used , the wast is dumped at major engine terminals into general sewer system.
On older locomotives the toilet just dumped on the tracks and nature took care of it, even if 50 trains a day used a line maybe only 3 engineers took a dump anyway. so not much more than what the average dog walker leaves on the railroad.
On steam engines the just dumped on the shovel or pee on the coal. and the evidence disapeared in the firebox.