Anything installed with screws is not a permanent install. You may need to replace or remove one (or both) for some reason in the future. You are using the product to seal the holes, not hold the tabs on the boat. Both are designed for use below the waterline. I have seen 5200 damage gel coat and fiberglass during removal. If you want to use it on your own boat, it's your boat. However, 5200 should not be recommended as a sealant to someone that doesn't know any better (people seeking advice here) because it can cause serious damage when removed.
4000 is also rated as a better sealant between metal and fiberglass by 3M. It also maintains better flexibility (water proof properties) while 5200 becomes rock hard and can more easily produce fissures that leak. Polyether (4000) also has very good resistance to oils and acids where 5200 has very poor resistance. 4000 is also rated as suitable for more materials such as glass and Lexan where 5200 is not recommended at all. Bottom line is if you are using the product as a sealant, you should use 4000. If you need to use the product as a bond to carry weight without any other mounting mechanisms, then you might consider the 5200. However, in many cases (depending on the materials) the 4000 still provides a better bond and better resistance against deterioration.
One last item to point out: the 4000 is better suited for vibration as it is not as brittle as the 5200.
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How to Select Sealants and Caulk | West Marine