I had mine done and they told me the same thing. I can't tell a difference, and the new ones look great. The reason they tell you that is because the factory has a machine that does it, where the dealer has to do it by hand. I guess they're covering themselves in case you don't like them.
I don't think the stitching changed color. To me it looked like the spool of thread had rust or something on it when the vendor stitched the covers.
I hate to say but maybe you should try another dealer for warranty work. I had to do this before when I had a F-250. One dealer treated me...