Correct me if I am guess incorrectly, but your 2016 F150 is the aluminum cab. My 2018 F150 has similar material in that body weld section. Look at other F150s and you should see the same material. It in most cases is not perfectly smooth as your is showing some irregular surfaces.

Your photo to help is the top of the truck and that zone is where the body is bonded together (in your rain gutter).

Most likely this truck spent it's life out in the open air under a tree and those black spots are stained. If it is aluminum cab it is not going to rust.

You might want to use the toothbrush and some mildew remover as Spikey Mike suggested. I would not be too concerned about marring the paint in that channel but if so you will have a bigger job to polish in that rough area.

Oh well at least it is on the top and out of sight.