comments:
I use two-part silicone putty to modify or expand store-bought silicone molds and it works great. I see no reason it wouldn't work here to seal up the hole tightly, but also in a way that you can reuse it. There are tons of brands and craft stores do stock it in the resin section, but you can get it off Amazon, too. Alternatively, you might consider using the technique used for earring posts? Using the putty, attach a silicone "bar" to the inside, to act as negative space. That way you don't need to fight with sealing the hole, and just insert the dowel after it cures. That'll also prevent air bubbles from escaping the wood. The hard part might be de-molding it without tearing the bar off the side, but I suppose that only matters if you want to reuse the mold repeatedly?