The kit came with extra sealant to address the side rails. I skipped it, but mine sits down lower and allows the rubber skirt to contact the plastic cap. Mine has to be in a car wash to get as much water in as your photos show.
My truck got blessed with snowfall in a state with a lot of love for mag-chloride in its first week. Yesterday (as soon as the roads were completely dry, it got an autowash at a touchless place. No issues to report. Didn't need to fold the mirrors. The F250 ahead of me looked wider with them...