I usually start by tapering the overlay as much as possible before gluing it on and make sure to wipe off the glue at the end of the taper before it dries. It just takes a lot of patience. A light sanding on the glass isn’t going to hurt it, just try not to get too deep.
I tapered the Walnut on this one and left the antler untapered because I could work it down without getting into the glass.
Dennis
My riser overlays start out no more than .040″ and usually .030 or less. It doesn’t take much sanding to blend them in. Use a flat piece of wood to back your sandpaper.