I went through about the same process as you are doing with the same results.

I then used copious quantites of 3M 5200, putting an approximately 1/16" thick bead around the whole boat (except for transom). The bead is the width of the stainless gunwale strip, so when the strip is remounted, it will cover the 5200.

In three years I have had no problems. On occasion a mooring will pull out a screw, but i simply replace it with a new screw, mounted in 5200.

My understanding that the junction for new boats is frequently secured with 5200. It is strong enough to do that. Where there is a significant hole,, such as shown in your picture, obviously the 5200 "fill" is more, but it is still 5200.