This pan and bulkhead is not structural, however it is also unusual for these rivets to fail. You are probably not "Pulling the pilot house down". The pilot house sides and top of the dog house, and for and side decks and gunnels and splash well are all molded in one piece. The roof of the pilot house is a 3rd moldment and the console, shelf over the entrance to the V berth/bulkhead is a 4th moldment.
I suspect that if any sealant used there it was the Bostec or similar sealer/adhesive, similar to 3m 4000. It would be questionable that the 5200 would adhere to both sides, without removing all old sealants, scraping, cleaning and be sure it was down to clean gel coat. If a silicone was used, then any chance of adherence is gone.
I would go with SS bolts and lock washer, then acorn nuts, or single SS nut with blue Loctite. Not sure why the rivets failed, but, if you use self taping screws there is a good chance they will also fail. (Due to cause of other rivets failing). Has any salt water gotten on the rivets?