I just received my new mahogany boomkin and rudder cheeks. I am going to seal them with penetrating epoxy like I did for my bowsprit. I was wondering if it would be acceptable without losing any strength to over drill the bolt holes by about  1/8” and fill it with epoxy and then re-drill the correct smaller size for the bolts through the solid epoxy. I do this for deck hardware but just wanted to get someone else’s thoughts on doing it to the boomkin.

Instead of overdrilling why not use a low viscosity epoxy (West Systems) that will 'soak' into the wood.

It is how I sealed the bolt holes in my new bowsprit.  I further thinned the West Systems epoxy a bit with a small amount of acetone and 'painted' the interior a few times with Q tips.

Additionally I 'countersunk' the holes and used butyl rubber tape under the washers and/or bolt heads.

I recommend using a drill bit 1/32" larger that the bolt size.  Tape the underside of the hole, pour in thinned epoxy resin, and let it sit a while.  Before it hardens, pull the tape and drain out the excess.  You should have a good coating of epoxy on the walls of the hole, and the bolt should easily slip through without having to redrill the hole.

Just my humble opinion, after building a few hundred boats.