Jason, i set spots on leather that is not thicker than the prongs are longer.
I have one of the spot setters i would like to sell.... I had the same problem as you have.
Now i use two wing dividers, one to mark the distance between the prongs and the other
to mark the distance between the spots.
after the leather is marked i will use my AWL to cut the holes for the spot prongs.
this works for me........