I've been told that the "miles left til empty" estimate is pretty deadly accurate. Driving it down to <5 miles left is essentially 1/4 of a gallon. You're fine there.
This doesn't change anything. Warrantied work is warrantied work. Unless somehow your supercharger is responsible for corroding the paint, they can and should fix it.
Now... if your issue is not wanting to leave that sort of massive power in the hands of some inexperienced tech, then I...