I find that what customers usually mean when they say the "same stitch holes" is the "same stitching line" - which is doable. This may not be perfect every inch of the way, but at Leather CARE Specialists we're pretty good at compensating for leather layer movement. But to say, and mean, "hit the same stitch holes", that's probably not doable for the entire length of the zipper. Oddly enough, this is especially true for the best made jackets. That's because the better the jacket was made, the harder it is to get apart.
Whenever you have to pull something apart the leather stretches and pattern pieces separate. So when we tape the pieces to the new zipper, we'll ease the leather back in here and there for a consistent look. We set the stitch length to what it was originally and start out hitting the original holes. Then whenever the stitching gets off because everything has shifted, we'll make an adjustment and move forward again. All with care and caution.
Also, and maybe it goes without saying, but since we are sewing the underside facing blind, it may reflect a new row of stitches there. When taping the back of the zipper to the facing underneath, we do try to place it so that the needle will hit it's original stitch line as well. (Unless the zipper was not put in well to begin with. If it wasn't, we will correct it's placement, intentionally throwing the facing's new stitch line off of it's original one). This is tricky and takes some time.
Ultimately, the leather we can see and have the most control over, should look pretty great. The hidden piece, maybe not so much. Obviously since we have to make a choice about which piece of leather will look the best- front panel or facing -it has to be the piece that shows. With a jacket that the top folds over, you'll want the facing to look the best for some inches. With that style of jacket we'll stitch with the facing on top to where it folds, and then stop where the stop-and-start- will not be seen, and turn the jacket over and continue stitching with the front panel on the top.
As for functionality, the zipper needs to be set far enough away from the leather that the pull will slide easily and not rub the leather, while not being set so far out that the tape is overly exposed, or not caught. The placement of the zipper between the leather layers where the zipper's box and pin are is critical, and is calculated to a 1/16 of an inch. If it's too close to - or -too far from these mechanisms (even if the tape is caught securely), it will be problematic for both the simplicity of use and the life of the zipper.