Why do some sets contain parts of an unrelated colour that are hidden on the final model? With recent and current sets, I noticed that some contain parts of a totally different colour than the rest of the set. An example is 8200-1: Radiator Springs Lightning McQueen, which contains a blue 2×6 plate, 3 yellow 1×2 plates, 2 white 1×2/1×4 angle plates, and 2 grey 1×4 plates, while Lightning McQueen is red. 

Parts like these aren't usually visible in the finished model.

Why are they used?

These are parts that should be available in most colours, including red. Did they have an overstock in these colours? Is it to make for easier building? Since this way both the model and the instructions aren't a big blob of red?
I believe the main reason is so that the pieces are easy to identify in the instructions - as many LEGO sets don't have the Technic style "List of elements used in this step" it's always a fun game of "Spot the difference" to see what's changed:



If those pieces were all red, then the target audience (5+ on those sets for example) might find it very frustrating to build.

(Even with the list of elements to use in a step it can often be quite an effort to find where a particular part goes.)