I can only speak for the rails on my '01. They are aluminum and the paint failed. I use a rooftop carrier from time to time but do not think that to be the cause of the problem. Simply put, Ford famously does not know how to paint aluminum.
When I decided to refinish the rails I opted to use pick up truck bed liner. One aerosol can was enough for the job. When I was at the auto parts store, the guy behind me in line offered great advice on painting aluminum. For prepping the surface to bare metal he recommended scotchbrite abrasive pads. Apparently sandpaper leaves a surface condition on aluminum that is adverse to coating bond. Turns out the guy was a retired Sikorsky Helicopter tech with career experience in aircraft aluminum.
The bedliner worked out great. It has a sanded texture that built up nicely. Cargo stored on the rails doesn't slip around and can't scratch the bedliner. The coating has a factory appearance that still looks great years after I did the job.
I realize that your question was about care and maintenance, but failure of the rail paint might be inevitable on your Expedition.