All of a sudden, my 2011 Overland with all-terrain package started making terrible grinding noises whenever the transmission was in drive or reverse. It sounded like a garbage disposal trying to grind up a rock. The car drove fine but I thought something was getting destroyed, so I took it right to the dealer.
Turns out that a small rock had gotten lodged between the transmission case and a skid plate. It transferred the normal transmission noise to the car body, which amplified it. I must have picked it on my 900-foot gravel driveway. There was no actual damage.
So there's one possible reason not to get skid plates.