Those are for the Original seayt mount, well they were on my Fat Boy I put on a mid frame chrome cover. I think you can also mount a second pair of footpegs which gives passenger another riding position.
Seat mounts for the stock seat on a Fat Boy. My Mustang set doesn't use them but I think they are hidden under the seat now. Seems awful high to put an extra set of pegs on.
Not sure what they are for but a quick fix would be to the hardware store for a rubber style plug, or maybe even some black silicone. Not exactly the custom bike fix but it would fill the hole and make it much less noticible until you found a better solution.
MikeM