number one ; the only thing that prevents rot is epoxy ..but only if the wood is dry before hand ,,under 12 % moisture,, or it will rot from the inside out if the wood is encapsulated.. epoxy soaks into the wood & prevents water molecues from penetrating.. chaulk may seem good but doesn't penetrate.an can peel away or have a void ..polyester resin is not a glue, does not truely bond to wood & lets water molecues pass rite thru ,, doin' nothing to prevent rot.. for bolt holes or for any hole in wood is a bad thing .. an is a gateway for rot.. especialy because a hole exposes the end/side grain like a sponge.. oneway to solve this is by goin' to a good hardware store an buying some brass tubing made by K & S .. it comes in vast fractional sizes.. say for the motor bolt holes in the transom buy a larger size tubing to the size of a standard spade bit..bore hole in transom cut a piece of tubing the thickness of the transom shy a couple mm's.. mix & apply epoxy in the hole/s then apply it again before set up.. soak it good. then apply epoxy to the cut brass pieces slide them in the hole/s .. that's it sealed hole for life.. then you can put bolts thru after cure & chaulk the play left in the hole/s...TIP... vinger cleans up uncured epoxy like nothing else & it's cheap & safe.. hope this helps