Would there be any harm in just removing the bolts and filling the holes with sealant
and then replacing the bolts. There doesn't seem to be a danger
assuming the holes in the floor are sealed and the water
can't run into the core
of the floor. If it stops the leak you solved
the problem and if it doesn't you take the thing off and seal the entire binnacle. While not as likely to fix the problem it is easy to check after you do it to see if it worked.