5200 is clasified as a sealant, with adhesive properties. It is not intended to fill gaps or holes. (Although used for this at times). When 5200 adhers, it is a good adhesive, but there are times it does not adhere.
If you look at the technical bulitins for 5200 (all of the 3M materials) There is a table for adhesive properties. It is not as good as epoxies by a long shot.
I personally do not use CPES in the filling of hull screw holes. If it is dry, there is not reason--and the use of undiluted epoxy is optional.
As for the filling of previus holes inn the deck, there are several reasons not to use the 5200--including it will discolor with time (4000 does not discolor as much, but is even a poorer adhesive).
For bolt holes, I would want to use some structurel material--such as glass fibers if the hole is 1/4 inch or larger. Gel coat can be used with epoxy-and in small areas, a gel coat paste color matched is probably a good product to use. There is also the option of using thickened epoyx, then using a Dremel tool to contour the surface to replicate the non skid surface if necessary--finally liquid gel coat to finish. There are other ways, including using non skid pattern molds, making your own mold, and dabbing on thick gel ccoat paste then contouring it.
Perhaps the best product is vinyl ester resin, which is compatable with gel coat, and stronger bond than polyester resing. There is a lot of personal prefernce--but I would never use 5200 as the primary filler for a hole.