You can just put the stock bolts back in place or get some grub screws and use some silicone to seal it. Then it will be completely flush to the roof. The threaded inserts can only be removed if you drop your headliner as the the part on the roof is flat like a washer, poking thru the roof and then the interior part is a long nut that threads and compresses it.
You probably won't escape the imprints/marks left behind from the rack that may not polish out, but again even lowered I cannot see the top of my truck. I did put the Esky rack on which covers it up, but it does look sweet naked though.