Well, there oughta be enough holes for snaps for the tonneau or boot cover. Any filler in that area? Perhaps someone filled around there and then, for whatever reason, randomly drilled holes they thought would be useful for snaps. It wouldn't be the first time I've seen that.
I remember once convincing a buddy with a Spitfire MkIV that he "needed" a nice tonneau cover for his car. (Ok, I just happened to have a nice tonneau but had no use for it!) He went for it...and I spent about an hour carefully probing around the top of each door to find the three tonneau snap holes that I knew had been there before he'd had the car repainted. Found them, riveted in new snaps and he was set! :wink: