If you want, you might be interested in looking at my album about the rebuild of my oday, including the note i made about sealing and painting the bulkheads. If you seal the edges with epoxy, and the edges of the holes that you drill for your chainplate bolts, then it will affect your stain, so be sure that you don't get sloppy and get epoxy where you don't want it.
Also may take a look at how i redid the deck where the chainplate exits. I built it up with fiberglass mat. I also cored out the deck there and filled it with saturated mat, then filled the whole area with thickened epoxy.. Be sure to bevel the outer skin so that when you put the chain plate cover on the beveled area forces the sealant of your choice down into the gap. That is the same bevel we should be using every time we reset hardware. It is illustrated in Don caseys series.
Finally my experience with the chainplate was that, even though i was very very carefull with the 3m 4200 sealant, i still developed a leak in my chainplates, both sides. The reason is that, as the mast and newly installed bulkheads settled into their new positions, (if you take a look at my album you may see what i mean, because i redid the deck at the base of the mast, so everything was at a slightly different position than original when i put it all back together) there was a little more movement at the chainplates than what the 3m 4200 would allow.so all i did was dig out the 4200, and sanded and cleaned the deck in the affected area to get a good seal for what i used next. And that was butyl tape. That was three months ago and still no leaks either side. So far all the things i have seated with butyl tape has not leaked, I love that stuff, and it is cheap, and easy to clean up.
keith