I had a little bit of a time getting my blue S, so I appreciate getting the color/options you want.
If a dealer can get one in your exact choice at a great deal, scratches are super easy to take care of, assuming in the clear coat still. If you don't want to do it yourself, there are plenty of really good detail shops that will make it look better than new, literally.
I know the whole changing incentive thing, but odds are you will not get close to the same deal as buying from inventory or dealer trade. I've ordered quite a bit of cars, and one thing they should be able to do is give you a % off plus whatever incentives are offered when the car arrives. All of my Audi and Porsche orders have been taken care of like this.
Everyone's different, but I personally would go for one that's here with a set 'good' deal, and would use any imperfections as a negotiating piece. If it's a reputable dealer, they will understand you don't want swirled or scratched up clear coat.