I had the same grommit perish and drop out of the hole on the underneath edge of the tailgate. I took my car in to the dealer and they replaced it no questions asked. Apparently its common for the grommit to drop out of the hole.
The first time I notice it was missing was when i had washed my car and noticed water trickling down the side of the tailgate from the seam of the plastic inside cover when the tailgate was open. I now have the new one fitted and no problems with water trickles inside the boot since. I can confirm also the grommit is to hold the drainage tube in place.