I can speak from personal experience that I DID have a problem on my longarm when I put it on upside down. The needle pushed little tiny tufts of the batting through to the backing. I don't think this would happen to a hand quilter but it could easily happen on a DSM (domestic sewing machine) and most definitely will happen with a LA based on my experience and others.
A little rhyme that always helps me remember with W&N is "Bump side up"