Amanda, you are right, the scalloped edges can increase the chance of gouging your cutting mat. Although, I have done small jobs on the top side without problems. But Laura Wasilowski recommends using the back side of the mat.
@amoret - i have cut all of my pieces for 3 bed sized quilts (mostly 1 1/2 inch squares and fairly short 1 1/2 inch strips) plus edged quite a bit of fabric for prewashing and also finished a couple of little projects all using the scalloped edge and i haven't noticed any unusual wear on my green olfa mat. i hadn't heard that before, though, so i'll start to really watch for that.
i have fallen in love with my scalloped edge rotary blade. i read a tip somewhere that using it to trim the edges of fabric before you pre-wash will cut down on fraying in the washer. i tried it and really liked the results. when i got ready to cut my fabrics for a small project the blade was already in the handle and i decided to give it a try again. i loved how the raw edges all stayed so neat and free of hanging threads as i worked through the project. i'm a stickler for precise measuring and cutting so it surprised me that the wavy edge didn't make lining up edges trickier. actually, i felt like it was actually more precise. my pieces don't unravel as i work with them and everthing seems to stay so much neater. i use the scalloped edge blades almost exclusively now. ( i am using the blade which produces a rounded off version of a "pinked" edge. short, shallow waves)