My eyebolts were already 1/2", but (apparently) an older style of 1/2" that didn't screw to the deck, so they could still rotate. Some clearly had, and had leaked at some point, but not enough to really impact the core.
With a 1/2" hole already, it was easy to get a dremel head in to grind out some more core (without over-drilling the fiberglass skins). I filled with epoxy and re-drilled, all at 1/2". Hope that made some sense.
For the screw holes in the eyebolt plates, I didn't through-bolt. But I didn't want screws straight into the wood core. So I overdrilled those (maybe to 1/4"? I can't remember), filled with epoxy, and put the screws in covered in wax while the epoxy cured. That makes something of a pre-threaded epoxy mount point (with sheet-metal threads from the screws) that you can screw into when assembling (and still get the screws out if needed).
More recently, I've done something similar for other screw-mount items, drilling ~1/4" holes, filling with thickened epoxy, and tapping machine threads into the epoxy. That method seems easier and less time-sensitive. And we're not looking for a lot of pull-out strength. Just enough to keep the bolts from rotating.
I think I recall a Practical Sailor article comparing the strength of various mounting methods - tapping into thickened epoxy isn't super strong, but not bad - plenty for this application. It's stronger if you shove some fiberglass in so you're filling with a mix of glass + epoxy. But that's probably not needed here.
It will take a few rounds of tightening with a torque wrench (over a few warm days) to squeeze out all the butyl and get your bolts tensioned right. A few more notes at
my original post, but I think I said it all again here.