The only way to seal these holes is with an epoxy. If they are small, then the Marine Tex solution is OK if done properly This assumes that there is no water in the transom core.
First I would determine if there was water in the core, by drilling the hole slightly larger than the screw threads. You can then look at the small amount of wood which comes out and use a metal pick to feel the core. If the core is wet, then you need to drill the hole out more; enough to get a Dremel tool bit or a bent coat hanger in to remove that wet core.
After the wet core is removed, then coat the dry wood (Balsa, plywood, or even foam in the newest boats), with thin epoxy. then fill the hole with thickened epoxy. If the hole is fairly large, then I would use mill fibers (glass fibers) in the mix, cabosil and a medium filler to peanut butter consistency. Fill the hole and under cut--then fill flush to the surface, and fianlly sand out a little beyond the hole, put a final layer of filler (no mill fibers) let it set up, and sand it smooth.
If no water, then you can work Marine Tex into the hole, and also grind or sand it out at least 1/4" beyond the hole--fill all of this, and then sand smooth and go ahead with the Sternmate.
Having gone to all of these efforts---It will probably be cheaper and easier to just do the Starboard mounting board.
