I didn't know they did, but I suspect maybe they realized certain colors just won't look good with the look of the CS. The red lettering on the tail would not look good in twister orange. I'd be willing to get the green is out as well, and possibly the reds. Gray, black, white - those would look good.
For me that boils down to the question of how often I might take the car to the track. We don't have a lot of tracks as far as I can find in Pittsburgh and they seem on the pricey side (to me), so for me it's the look and the feel of a Mustang. So I think I'd be happier with a loaded GT/CS than a performance car.