I pulled the stock roof rack and I'm in the process of grinding the screw inserts flush. I went to far on one and it fell through. I currently have a hole about ~3/8" in diameter on the front left side of the roof.
One thing I've thought of is somehow lowering a bent strip of steel in through the hole with adhesive on the sides and attach it to the inner side of the roof. Then at that point it could be somehow sealed.
So far for the other roof rack holes I've been red locktighting a grub screw in the flush screw insert, then sealing with Quick Steel.
Any suggestions are welcome.