I carry a spare in the bed and the spare under the bed. I have never had an issue with the spare under the bed dragging on anything. Personally the tire in my opinion helps protect the rear. Otherwise the only item to catch without is the bumper and I have seen guys tear their bumpers off. I have torn off the trailer plug and the lights I had under the bumper even with the spare under there. I plan on keeping the spare under there.
Now I have had plenty of flats, plenty! It is extremely useful to have easy access to your spare as sometimes trying to get your spare from underneath when on a trail is a royal pain in the ass. Later when we get to a spot that is better and we have time or at camp or parking lot will then put the flat underneath and move the good spare in the bed for the next flat.
Of course if it can be repaired or patch do that but I have taken my sidewalls out too.
I did relocate my trailer plug into the bumper.