The Scot should be resting primarily on large rollers under the centerline of the boat. The centerboard case is well reinforced and should bear all the weight. The bunks are there to keep the boat from rocking side to side and bear very little weight unless your are cornering hard.
Thus the bunks can be carpeted or rollers, it doesn’t matter much. The trailer bunks and guide rollers should be arranged to guide the boat onto the trailer. You want to be sure the center keel is on the center rollers.