I don't think you will get rid of the rough bottom stitch through adjustments. As in another post on the site, the needle slices/pushes leather down and out along with the stitch. I wet the backside of a belt and use a roller to smooth out the bumps. My stitch on top will pull level with the leather without making a stitch groove.
After posting yesterday, it occurred to me that most of us use smaller thread for the bottom. My question would be to those who use, for an example, 277 top and bottom. Do you get nice straight buried stitches on the bottom?