The best answer has already been given by Dave, but in woodworking we sometimes hide our mistakes by a mixture of white wood glue and sawdust (or the dust from sanding). This method ensures an exact matching colour. I don’t see why this method wouldn’t work with epoxy as well.
You wrote the mahogany of your transom is fading. A good sanding may bring some life back to the transom as well as giving you the right colour sawdust for the screw holes.