I was going to check my seat last night, but anyway skipped my mind but i didn't notice anything that caught my eye when I pampered my leather and installed weathertech mats.
Did you check your spare tire? I would not consider this normal in any way and would expect Ford to either fix or buy back (under 500 miles is still a new car, don't put too much miles on it until you get a response...). But, that is just me and might not really happen, they might just tell me to fk off. If it was a spot of rust, i'd just buy something to treat it, but since its all over the untreated metal of the vehicle, uh.. I rather not, and since we are both OCD, this is really hard to let go.
Will it affect anything? not in the next 5-10 years, would it bother the heck out of me? Yes.
I would:
Check for sunroof leaks
Skip the dealer because they will just give you the run around or just some half baked answer 98% of the time, I have never once had any dealer resolve my problem perfectly without manufacturer getting involved, so I learned to just skip that and go straight to manufacturer.
Try to recall how many miles were on the car at delivery (more = more time spent on the road = more potential of some test driver left the sunroof open and it rained...
Call Ford, I heard they are pretty good to deal with.
I'd never buy a car with a sunroof, personally, like, you even if they paid me the value of the sunroof, I won't take it. Free car? Sure. lol (I have something VERY against sunroofs.. I am not blaming the sunroof, but its a chance!..)