I am thinking really hard rubbing to get scratches out could affect the dye?
You shouldn't have to rub really hard. If it is just a light surface scratch which is usually the case on box, it should take the polish well and look better ASAP. If it is really a deep scratch, then it will stay there, but should look a little better. It is better to polish, wait and polish again. Each time with a light rub. If you are applying the polish thinly and letting it dry completely before the buffing, it should work well. I think that the boutique is doing the polish/buff process several times when you bring it in. People tend not to have the patience to let the polish dry properly before buffing. Rome wasn't built in a nanosecond!