It shouldnt be a hassle for you, since its warranty work they should give you a free rental while they fix it (at least thats what they do at the dealer I go to). As for the spot fix, they dont usually do that with clearcoat. Thats why most touch-up paints are so hard to match, some colors look different depending on whether or not it has clearcoat over it. I'd say take it back to the dealer and have them fix it, otherwise its going to irritate you every time you see it.