You can get some rests to work with the low holes. In my case I was originally trying to use a QAD HD but with the low holes I ran out of vertical adjustment and the launcher arm was smacking the shelf before dropping all the way flat. If you use a rest like a G5 Expert that falls behind the shelf it will work. For me, I'd rather have that extra 1/4" of vertical adjustment.
What you need to do when tuning is forget about trying to set your arrow through the center of the berger holes, you need to be about 1/4" above the center of the holes.