After SO MANY hours spent making the metalwork 'just right', it's almost sad to cover it with filler. The key, of course, is to use as little filler as possible. No 1/4" (or worse) patches that could crack after a harsh bump. No filler on parts that are stepped on - or that take a lot of weight. And definitely, no filler on the truck box floor!
Of course after final sanding, much (or all some places) is removed, leaving only enough to make the primer lay down straight enough so that final blocking presents a perfect substrate for paint.