I had the same problem when I got my Bed cap, it was even specced specifically for my model year (07), when I took the spoiler off the holesleft were horrid and the cap didn't come any blanks for the holes, so I modded the bed cap window so the spoiler could go back on.
Not sure if you'll find anything specific for these, I'd say you've got 4 choices:
1 Find something that fit the holes to blank them of by trial and error, but it will still look messy.
2 Go to the expense of having the holes filled in properly and the tailgate resprayed
3 See if the earlier tailgate without the spoiler will fit your truck and find a matching colour one from a breakers.
4 Have the tonneau cover modded and resprayed.