Not sure if this is posted in the right spot but, I recently did a roof rack delete and sealed the screws back in. My question is is there any chance of leakage between the threaded insert and the body as this was covered up before or are they water tight?
I know there were a number of people who did this mod in the past, don't remember hearing anyone talk about having leaks down the road. You could always put a small smear of silicone on on the underside of the screw heads and put them back in to ensure they're water tight.
I used some RTV silicone a while ago when I took the roof racks off of my Rainier for a bit. No problems with leaks and it was raining a lot at the time. Just make sure you fill the holes and try not to use too much in case it starts dripping onto the headliner. It's a little harder to completely remove the silicone in case you want to put the racks back on but it looks a bit better than the protruding bolt heads.