I just pick a spot that is usually in the neck muscle. When it approaches the temp I'm looking for, I probe around the butt with my impeccably accurate BLACK Thermapen. When most of the butt is at the temp I want I pull it from the smoker.
A few small holes in the foil make no difference whatsoever.
Operation BBQ Relief Founding Member - I am Obsessive Compulsive about BBQ. Google it.