Jeep has improved the insert nut mounting hardware. It is a PVC coated molly style nut/insert now, no rubber. They are far supperior to the old style nuts. They will not pull out under stress or age like the original rubber/brass inserts. I just replaced mine.
However, if you do not have the holes in your roof already I would seriously consider getting different racks that do not require holes in the roof. I have read here that there are several styles and supliers available with better quality and heavier duty racks than the OEM jeep roof racks. The after market ones attach to the roof rain/drip rails (or what ever they are called) and do not require holes in the roof. Also it is very difficult to drill the holes in precisely the correct spots, and they must be drilled in precise spots for the racks to bolt up correctly.