The issue with silcone is not that it doesn't work as a sealant but what the residue does on the boat. It is almost impossible to clean off even if you can't see it and even the tiniest bit of silcone residue will prevent paint or other finishes from sticking to wood, fiberglass, you name it.
It is also a bitch to remove a frame or something sealed down with silicone in our experience. Sikaflex, while as good or better an adhesive/sealant as silicone, for whatever reason makes a bond that we have found to be far easier to separate. Which makes it far less likely that something like a wood window frame will be damaged in the process. Of course, Dolfinite makes removal of a frame even easier.
But the real problem with silicone is that once it gets on something, particularly somehting porous like gel coat or paint or whatever, it is a MAJOR effort to get rid of it. Far, far easier to avoid the potential problem altogether and simply not use it. Particularly since there are plenty of adhesive sealants on the market that are as effective or better than silicone but without the non-stick residue problem.