By sticking with regular trailers instead of intermodal boxes, they don't have to worry about equipment imbalances and chassis availability at different points. Also, not all trains are double-stack capable, especially in the Eastern half of the country - too many tunnels and other height restrictions. Also, I've seen occasions where a train gets stripped and the boxes stacked up, which limits access to the ones on the bottom. With wheels on it, the trailer can't get buried at the ramp as easily.