There are alot of different factors that affect the use of the rear mud flap. Always, first make sure the mud flaps inside the fender well are long enough (about 5-6" off the ground, and wide enough (1" past each side of the tires) to work. The rear mud flap can help catch the other 20% of the rocks that get past those mud flaps, but it must stay at least 4" off the ground to avoid throwing rocks at your toad.
While following our Dutch star, which has both the wheel wells and the back mud flap, I found that the exhaust faces the ground, out the side, and is blowing up any and all loose dirt along the road edge. We are looking into turning the end of the exhaust sideways instead of down toward the ground to try and take care of that dirt.
As for the back mud flap, our last trip we went thru some roadwork with fresh tar. No doubt that rear mud flap did the job. It was coated with tar, but the CRV on the back was totally clean of tar. We have taken the toad over 20,000 miles now, and no rock chips to speak of.