There's no hole in the window. Inside piece of the antenna is double sided taped to the glass and the outside is double sided taped to the glass. Just take them off, clean off the tape residue and tuck the wire behind the interior panel. You'll never know it was there. I took mine off before I had the window tint redone. The only reason they show a different part number for the backglass for the OnStar cars is because it comes with the two halves of the antenna pre-applied to the glass, the window itself is identical.
As for the antenna on the fender in question, you will probably have to pull back the trunk carpet on that fender and remove the nut holding the antenna on. Pull the antenna out and discard. Have the hole welded shut, bondo'd, sanded and the fender repainted.