I've been pondering this, and the main issue is the "punch-through" that occurs on the backside of the leather. So, use the machine, with no thread, to pre-punch the stitch holes. Then flip the work piece and do the same thing from the backside, into the same holes. This should even out the "punch-through" and by then when it's run through the machine again, with thread, it should be better on the back (hopefully).
Personally, if I want something to look hand stitched then I'll hand stitch it.