What is the best for sealing the perimeter screws that hold the cockpit floor down (removable floor) bolsters and other misc screws.
Method of applying? Coat the screw? A dab in the hole? Tips for avoiding a mess and clean up chemicals?

I use 3M 5200 for screws into wood. Can shoot it into hole or coat threads, don't think it really matters. Have lots of paper towels handy and a bag or can to put the dirty ones in. It wipes up fairly easily from gelcoat when it's still wet.

I would do the 3M 4200 just in case you need to take it apart later. The 5200 is strong stuff and i have torn gelcoat off transoms removing trim tab plates!
Also look the fast cure versions. i found out the hard way the standard 5200 takes 7 days to fully cure! I have only found the 4200FC (fact cure) available locally so i'm not sure if they make a slow cure version of that one.
Another tip is you can use WD40 on your finger to wipe it nice and smooth after you put it down and tighten it all up. Obviously don't spray the WD40 on the surfaces before putting the 3M stuff down or it wont stick! lol
Acetone for cleanup just dont sit there too long with the acetone or you will start dulling the gel

4200 max (if that)
If the screws still have good bite your sealer is simply to stop the screw working loose .
I use boatlife lifecaulk religiously . Screws don't work loose and when needed they come out when required without trouble .
A little injected into the hole or wiped onto the screw and you're ready to go .

LocTite PL S40 works great. It is a Urethane sealant just like 4200 and 5200. It is not a runny mess and a lot less expensive. I have also had good luck sealing it off and not ruining the whole tube. PL is kinda their "marine" product.
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https://www.homedepot.com/p/LOCTITE-...5293/203163736
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