Auto body repair & detailing: rust on roof, rust spots, ford expedition

Question
I have a 2000 Ford Expedition that has developed rust spots at the end of the grooves on the roof.  One spot is about an inch in diameter and has just started to leak.  Other spots are smaller.

Two body shops have recommended replacing the roof.  I am willing to do this but first want to make sure that there is not a simpler option that will provide a reliable repair.

Answer
This is a difficult spot to repair holes, at best. If you weld a patch over them, it will warp the thin metal of the roof to beat all hell, and to glue a patch in may simply be more work than putting on a skin. Try a couple more body shops, but remember, you get what what you pay for. Bill