The purpose of the mud flap eliminators is this- when backing up, or coming down over an obstacle just right, sometimes the mudflaps will get caught between the obstacle and the tire. As they are attached to the plastic bumper cover, this can result in having the whole plastic bumper cover being torn off while on the trail. If you remove just the mud flap to prevent this, you create a hole between the plastic bumper cover and the bodywork, which is likely to collect dirt and other crud which may lead to a corrosive condition. Mud Flap eliminators cover this void.
I modified the part of the OEM mudflap that attaches to the car so that no hole was created. Ymmv.