If you're still not convinced in the utility of countersinking the holes in your deck this photo was taken at year 8 of these pad eye's being installed and they still exhibited ZERO leaks and are still 100% bone dry.
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While you probably could use butyl below water I don't and use marine sealants instead such as Sikaflex 291 or a Polysulfide. 3M 101 is no longer marketed so you are left with Boat life Life-Calk as the sole marine grade polysulfide. I never liked Life-Calk as much as 3M 101 but it's still better than devils glue, AKA 3M 5200.
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This is EASY! Countersink, clean, tighten & clean up.... Done!