[Arran]

 That set must have left the factory with those extra holes in the side, it's highly unlikely that some owner would have gone to the trouble of measuring out and drilling such a neatly spaced set of holes that happen to line up with the alignment screws in that side of the chassis. The average owner wouldn't have had a clue that the padders and trimmer screws were even there, let alone what they were for. If the set really was a prototype of some kind I would just leave them there, short of replacing a good portion of the veneer on that side there isn't really any way to cover them up successfully. If you don't want to look at the holes just put the set on a shelf with some books leaning up against that end.
Regards
Arran