When its a set screw
A set screw is fully threaded while a bolt is only partially threaded. (And yes a set screw has a head. If no head its called a grub screw.)
This means a bolt fits better and thighter in its holes than a set screw does.
A set screw only have the sideways or bending strength of a bolt 1 size down.
A bolt can only be thigthened to a certain point because it runs out of threads.
Who knows if Spirit used set screws securing the plugs on a couple of planes because they ran out of the correctly sized bolts and expected Boeing to redo them anyway. Impossible to see/inspect unless you draw/remove the item in question. Or the head is stamped with a part number and you can see the head.
Should Boeing have overengineered it so that a bolt also was covered by a sleeve that double secured the bolt wasn’t overtightened and drew the frames closer, weakening them in the progress.
A sleeve would also protect the bolt from the roller pins it was supposed to keep in place constantly hitting it directly with potential for metal fatigue and breakage.
