For others who don't mind their reception dropping a little, I have used a $8 AM/FM antenna from O'Reilly's and zip tied it under the radio in the fairing. Then I had no visible antenna at all. This was very convienient with a detachable Tour-Pak. I would estimate my FM reception at about 60% of what it was with full lenght antenna. I usually use Sat. radio, so I didn't mind.
Not sure which holes you are refering to, but the TP has grommets that all but close the holes up. The left side still has wires going through it. If you are asking about the studs the masts normally attach to, I just left them as studs. I didn't run with the TP on much, anyway. Does that cover it, or did I miss something?
For others who don't mind their reception dropping a little, I have used a $8 AM/FM antenna from O'Reilly's and zip tied it under the radio in the fairing. Then I had no visible antenna at all. This was very convienient with a detachable Tour-Pak. I would estimate my FM reception at about 60% of what it was with full lenght antenna. I usually use Sat. radio, so I didn't mind.