When I purchased my new 2016 F150 back in October 2016, my truck looked almost identical to your photos underneath. I am ocd and couldn't live with the way it looked for one and I was concerned that it was an issue. Well, long story short, I learned that my truck was built in Michigan and the surface rust had to come from there. I think my truck was brought to the dealership on a truck and not driven. Regardless, I put a wire circular brush on my drill and went to town. I cleaned all of it up being careful not to screw anything up, and spot primed/ painted some of the worst spots. Of course I didn't paint anything where there shouldn't be paint (exhaust hangers, etc.). It looks great to this day.
I would bet the rust in those pics are just surface rust and will come off easy. I am sure if I never got under my truck and noticed, it would never be a problem, but since I knew about it I had to do something.

 

 

A wire wheel on a grinder, blow it off with air, then a few rattle cans of rust paint from the hardware store.
And like new.