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From the pictures I would suspect the roof received little attention during vehicle cleanings. It’s not uncommon for bird droppings or tree sap to sit and eat through the clear coat and paint over time which would explain those rust spots. However I could be completely wrong and it was just a defect during your trucks build. Bottom line is you had it corrected and it looks like they did a great job!I never found out what caused it. Now I have to have the cab checked out at some point, with the known F150 rust issue at the bottom. It kind of looks like someone repaired it, but I can't tell. Will post pics in the next day or so to get everyone's feedback.