Page 136 of "the book" covers bonding fasteners and resin bushing holes.
https://www.westsystem.com/wp-content/uploads/GougeonBook-061205-1.pdf
An excellent practice for all hardware on a wood boat. If all bolts and screws are drilled, filled, and drilled then all the better for preventing water from getting to the wood and causing swelling which will crack an epoxy joint in no time. Especially watch out for fasteners into long pieces of solid wood such as the transom beam.
For bedding compound I use butyl rubber and make a little doughnut of it around the washer of my fastener or on the contact pad of the piece of hardware. It oozes out nicely, seals the joint and does not harden. Same stuff they used to install windows in RVs. This much would least you for years and years. Store it in a plastic bag because it does dry out a little after the first year or so (like play dough).
https://www.amazon.com/White-Butyl-Tape-Mobile-Single/dp/B07BJLHH24/ref=sr_1_5?dchild=1&keywords=butyl+tape&qid=1593041102&sr=8-5
They also make a butyl rubber caulk which is more pasty for bedding things with more surface area where the tape which is more or a soft pliable rubber would be too stiff to be squeezed by the fasteners. So for something like the Eye bolt I'd use butyl rubber or nothing because it would only leak into the anchor well or onto the deck so it doesn't really need to be watertight.
Also be very careful when installing hardware not to crank down mindlessly on the nut our you will simply crush the wood and and thus crack the epoxy seal. I try to never use power drivers to install fasteners to the final tightness because it's so easy to over torque them.