I had the plastic fasteners left over from when I pulled the hood insulation mat out of my Sentra...they're just black plastic discs with little Christmas tree-shaped wedges on the underside. I expected them to stay in for an hour or so, but it's been at least a year and a half I think and all 4 are still there.
I also bedlined that portion of my truck, so they really don't stand out at all. I don't even notice anymore.
This is pre-bedliner.
EDIT: It just occurred to me that maybe you mean the holes in the rear bumper corners and the front upper flap area...where the lower flaps attached...gotcha.
Yeah, I don't have any suggestions there. I pulled the front upper flaps because my tires were rubbing them badly. Haven't done anything about the holes in the rear.