Agree, they look like screw holes from an old piece of hardware. If I were a betting man, it appears they may have moved the stanchion mount back due to striped out wood screws. Would fill then or drill them out and fill w/small bungs.
(edit: after looking at the pic again, the screw positions are a different spacing than the stanchion in the pic)
Related is to the screw holes in the cap is to check your stanchion mounts. Seen many that were just wood screws into the cap rail. IMO this is then a false sense of security
expecting the life lines keeping one in the boat
. If someone (an adult) fell against them, the stanchions will most likely pull out and that person will be in the water