Obviously, weathering, ultraviolet rays, and other environmental factors would have altered the paint shades after they had been in use for different times, and different chemical formulations of the paints over the years would have reacted in different ways as well. Also, there were some minor shade variations with different batches of paint, and railroads sometimes made changes to the colors they used on their liveries. However, railroads - or the paint suppliers they used - had paint formulas, specifically identified and numbered, to ensure that the paints used were as uniform as possible, and that the starting points for fresh applications were the same. There was nothing random about it. Here are the specific paints used by the Great Northern, for example:
I have read about this, most recently about handling paint issues on the Atlantic Coast Line during the purple paint era, and the effort and cost expended to maintain paints and uniformity. If one looks at pictures of passenger trains in their heyday, they show cars that are uniformly painted. They did not have multiple shades of yellows, or oranges, or whatever.
The model train manufacturers should maintain strong standards for proper paint colors; a "whatever" attitude shouldn't suffice. That's not what the real railroads had. And some variations done by model train manufacturers over the years are just off the chart. For example, compare the MTH KCS F units with the real thing: