The factory mounted the step fully below the body with a foam strip (F2TZ16536B) between them to protect the paint & prevent noise. On Broncos, the rear end wraps up into the wheel arch slightly. On Fs, the rear end wraps around the back of the cab; it never continues to the bed.
Note the extra body line at the bottom of the door indicating this is a revised door with a side impact beam.
This would probably be a good addition to the steps, if you can still find a set:
If not, the universal set is reasonably good:
