Have you purchased these 6 SVT vehicles from the same dealership over time? Or have you had no previous dealings with this dealership other than maintenance items?
Think where the dealership is coming from is if they just replace it and Ford denies the claim then they have to eat the cost. I would think if a dealer has been making money off of you for years, then paying for it would be more of a customer relations move more than anything. If the dealership doesn't really know you, I can see them pushing it off to Ford first to make sure they get paid. I've heard once your claim is in the system especially how many times denied, it doesn't matter at all if you take it to another dealership unless they just replace it and file later.
Said but true on dealership always looking for the next quick buck and not long term customers. My previous Ford had the emblem peeling and saw in a forum where it was getting replaced under warranty. My local dealership took pictures and submitted and ended up never replacing it. I purchased the truck from them. It was a $65 part so couldn't believe they just wouldn't replace it. Needless to say, even though that dealership is 1 mile from me, I will never go back. Granted I did bring my Raptor there too and when I was getting crappy service and other denied claims, it became my final straw.
I think your only choice to fix is to have a body shop remove it, sand it and paint.
There was someone that used some rattle can paint that matched nearly perfect in a thread here on the flares, so perhaps you can do it yourself.
And of course buy a new one and replace. I think they are around $800
EDIT: Did a quick search and found that paint flare thread
http://www.fordraptorforum.com/f11/flare-paint-32958/#post657629
