When you removed the screws was there wet, crumb like wood in the screw holes and threads? If not and it is dry, until you are ready to put the dorade boxes back in just put the screws back in with whatever removable sealant
you have. Epoxy putty is not really a sealant
. If you have nothing else, put the screws in and a tarp over the top. If you mean to hollow out the core by use of an L shaped bit and then fill with the putty it will probably work as it is supposed to be drillable but you will not be able to gel coat over the repair. We used epoxy putty to fill a hole in the deck that goes all the way through to the cabin
and no, we didn't hollow it out first, and it is still there 7,000 NM later and dry as a bone but I wouldn't screw anything structural into it. If you need a source for butyl rubber you could look for plain old grey plumbers putty, same stuff I think as the tape. We have a tub from the mid 1980s that is still useable. If you do use the epoxy putty you may not be able to get the screws out again easily.