The railroad business model is built on enormous economies of scale. You can move 5+ truckloads of a typical commodity in a single railcar. Now multiply that railcar by 150 cars in a train, and you have the equivalent of more than 750 truckloads of freight handled by a single crew.
But it sounds like the labor cost savings are at least partially burned down the line at the switching stations. Maybe it is more economical breaking down a 3x longer train than running 3 separate trains since the crew at the depot only works when a train pulls in. And yes I know rail is much more efficient compared to freight. I work with freight companies all the time, and overseas transport too.
And I do agree, if the train is hauling something potentially toxic, they should take extra precautions. I think Denzel made a mediocre movie about that (and I like Denzel, but that film, meh). There’s a TV show about a future world where the remnants of civilization survive on a train that circles the globe.