I work for an OEM automotive paint supplier. Ford is one of our many customers along with BWM, Mercedes, GM, Honda, Nissan and Subaru. If these defects are only on the interior I would definitely have them repainted at the dealership. These areas are painted for cosmetic reasons only and the lack of color there will not affect the durability of the finish. The aftermarket paint should last long after you have traded or sold your vehicle.
If you have exterior defects like this then that is a different story. I doubt Ford will replace your vehicle even in this instance. Most likely, the only thing they will offer and will pay for will be a paint job from the dealership. Carbon is no longer offered as a color on the Edge. Otherwise, you might have been able to negotiate a parts change with factory painted parts.