roof rack bolt hole defect leading to rust

The problem was discovered when I smelled standing water in the vehicle. I pulled up the carpet on the passenger side and underneath the carpet pooled water. I started by thinking it was the sunroof, I found rust all over it and the pictures you see are after the cleanup. I bought a new sunroof thinking that would solve the issue and blame it on Florida summers and move on. Next big storm, I smelled the water again. I had someone sit with a hose wetting down the sunroof area only and no leak. I had them spray all over the roof and sure enough I heard a trickle. I narrowed it down to spraying the roof rack. I pulled off the roof rack to inspect and all of the mounting holes were fine except one, that was completely rusted through and barely had support structure left. I wrote to Ford and was told to have the dealer look at it. I made a call to the dealer and was told I was out of body warranty and they most likely wouldn't be able to do anything. My frustration in the middle of summer in which we have tremendous downpours caused me to act on it and patch it up best I can. After cleaning up the rust I was left with a large hole. Body filler, primer, and paint was my solution. It was clearing a manufacturing defect in which the paint around the mount hole was damaged only on that one mount causing rust to propagate. My video link shows my progress.