All I did is remove the bolts with a torx bit and I washed the areas where the roof racks sat. When everything was nice and clean, I polished the surrounding areas on the roof. I painted the top of the bolts with black touch up paint so they weren't as noticeable and reinstall the bolts into it's original locations. Easy
TrainTrac, I havent got around to mine yet. The ones I had ready I put them on my wifes '08 escape. Same rivets as the trac. Actually what I did was ran a #6 metric die on them. You can shave the stem alittle. They are slightly larger than the screw. Sanded the tops so they would take paint. Scewed them in the rivet with rtv on them. They are flat to the the rivet and are the same diameter. This is the only brand I found that were perfect in size. Got them at pep-boys. If I see the wife today I will try to get a pic of hers. We are seperated right now. We are supposed to get together today.
As I said, I have a set for the trac. Just need to finish them. Been kinda lazy in that area, lately.
I didnt check the rivets on my trac when I put the screws back in. The rivets on my wifes ecscape were closed in the bottom of the thread hole. The only potential I see for a leak is the rubber seal where the rivet meets the roof sheet metal. I did se a trac one day that took the rails off. He did not have the screws in the holes. Either way I fill the holes to protect the threads.