Re: Symmetric Rudder damage and surprise hardware!
I agree with Faster, it could be original. I would leave the bolts in place.
Butyl would be a poor choice because it never cures, is oil based, and epoxy will not stick to it. I would just make sure the recesses are cleaned well of foreign matter, acetone is good for this. Fill the recesses with thickened epoxy and it should last many years. Stainless steel fasteners are used successfully when hardware bonding with epoxy so there should not be any difference in this case. I have not heard of epoxy separating from fasteners like this - probably just poor execution when the recesses were filled.
I have a few tools that have had epoxy on their metal handles for a few decades with no sign of separating.
Living aboard in Victoria Harbour