Will 5200 stick where there is silicone residue?

Commercial SeaBird Black Pearl. Screw in hatches leak like a sieve around the rim/lip and I've redone the silicone gasket/bedding once, but it lasts only about as long as it takes to flex the deck a couple times. Thinking about making the join permanent and sure but wondering if I can ever use anything but silicone now.

You say you've 're-done' the silicone bedding once. Did the manufacturer use silicone?
It is possible to remove silicone, with a bit of work. The first step I'd take would be to physically remove it by cutting and scraping carefully, from both the fiberglass deck and the (ABS?) hatch rim.
Auto body supply places sell solvent prep concoctions to remove silicone residue (from car waxes, for painting prep).
I tried using Sikaflex to glue a (snap-in) hatch rim once - followed the instructions 'to the letter', including the $$$ primer, but it didn't hold.
If I were to use a sealant like Sikaflex or 5200, I'd back it up with mechanical fasteners.
IMO, you have zeroed in on part of the problem - very flexy deck and semi-rigid hatch rim. The Tahe boats have a bit of a reputation for flexy decks and mysterious cracking sounds around my area; perhaps the Seabird boats are similar??