you can also weld something a bit higher right where the holes are now and sink the bolts, it would raise your transmission and t-case by 1/2 an inch let's say (don't know if you have room), you can achieve this with a 1/2'' flat bar in which you machine a recess about 1/4 inch or so, add that to your existing skid thickness and it's what the head of the bolts should be at. The other option is to use coutersunk bolts, you can probably get away with a 1/4'' flat bar welded to the skid in that case.
I like your idea and would add to the torque rotation resistance, my suggestion is just cheaper way (i think) and reuse your mount, don't mean or think it's better.