For a sealant, I would use a spray on lacquer. After 5+ coats it is pretty water resistant. I would personally do 7 or 8 coats on that piece.
You can stain and seal the cut-outs first (paint a little lacquer into the cutouts with a fine brush). Then stain the surface a few shades darker to make them pop out.
You can also reverse it and make them darker. Either way the contrast in color will make them more visible.