open the holes up a slight bit so you have more room. then attach a decorative plate on the underside and fill the hole from the top with suitable caulk, then put a cover over that and seal as normal.
tighter fitting holes provide less area for water ingress, but caulk works best if it has some play room, a wider strip of caulk can stretch quite a ways without splitting or tearing free. Once it splits it's a leak.
It's not a problem on stationary items, but everything bolted on to a boat moves.
stay away from caulks that dry hard.