I guess working in automotive I'm jaded to this. Some things you will just have to hit yourself like some members said with roustoleum. I don't expect a perfect product, because I know the overarching complexity. Since the bolts are not painted over this looks like it was caused by tightening them down.
Remember the chrome bumpers from the 80's? They were carriage bolts with the threads on the inside/backside of the bumper with nuts to hold them on. The nuts and threads were not even painted and had surface rust from day 1, but were not visible.
What you're looking at here is Ford's first year/s attempt at getting us a Jeep replacement. Those brackets will have the paint and/or design updated in the future because of complaints like yours. We know this bothers you, and it should also bother Ford, and it is just one of those minor things that will get addressed down the road.
Happy Motoring,