I found that there are only two-color double-layer cargo boxes on the sand table. There are many colors in real cargo boxes, red, yellow, blue, green, purple, orange... Although I know that the logo of the cargo box in the game cannot appear casually.
Most likely they did this to avoid using Generic Containers, since CSX does run their own fleet of 53ft Containers. Only other thing they could do is add the 40ft Containers, Hamburg Sud and Hapag-Lloyd, from the German Routes, as those do appear in the US on International Intermodal trains. Of course, another easy solution is to allow the 53ft container to be paintable in the livery editor. So we can have a real mix of containers.
No, not at the moment. People have requested the option to paint the containers but so far we cannot.