I would completely remove the hatch , set down a good quality masking tape, reset the hatch on the tape, trace its shape and trim off the area that will contact the deck , clean this area with a wax remover/ fast solvent , clean the hatch bedding surface as well, get a suitable weight ( sand bag), apply 3m 4200 ( its removable) vs 3m 5200 (is not), have some soapy water handy to keep your finger wetted . bed, screed off with your finger, set the sand bag , be sure it will not move the hatch,, and remove the tape also without moving the hatch,, you should be good, after it cures
I would go back with life caulk,but before putting it,clean everything and lay some 100lb fishing string down around the hatch and joint it together at a corner.Then apply the life caulk. If you ever have to remove that hatch,all you have to do is dig out the one cornner and pull up on the fishing string which will cut the caulking.
I went with the 4200..... the hatch also has about 20 screws of which I found 6 were stripped during disassembly.
So.... I removed the hatch....found that one corner did not have adequate coverage from the previous rebedding. Cleaned both the hatch and the deck very well....including a final wipe down with denatured alcohol. The hatch wood frame and deck were very sound with no rot.
Applied plenty of 4200 into the screw holes and on the bedding surface. Assembly hatch onto deck and used 1/2" longer screws in the stripped so they had renewed bite. Torqued each screw down lightly and let set-up for about 2 hours. Then came back and did final torquing in a criss-cross pattern. We had a driving rain storm a couple days later is all seems to be very dry.
JD if you ever encounter the striped screw hole animal you might try dilling the hole slightly larger then needed, getting a new screw or any mechanical fasterner, and apply some regular unthicked epoxy to the hile to prime it then after the primed hole cures mix up some epoxy with a little cabosil or other thickening material and then replacing the fastener, this will take care of the problem , and should you not be able to remove the bedded fastener apply some heat from a soldering iron it will help soften the epoxy and the screw will come out
Thanks for the great tips that you don't find anywhere except in the brains of those that have the experience. The soldering iron trick is especially interesting!