I’ve done the Artisan’s Clutch (came out great) and I think if you leave the leather it is cut from in place (hold down with magnets or something), you should be able to use it as a jig for holding the cut leather on the reverse side. I’m pretty sure the cut is symmetrical. So just include the initials to be engraved in the desired location when you do the initial cut but ignore the engraving, then flip the leather over and ignore the cut and set the initials for engraving. Might want to test in cardboard first to make sure this will work.
Oh by the way, check out the link to my clutch above–I include a design for a gluing jig that makes it easier to glue the leather to the plywood.