As an update, I rummaged around in my spares box and found that I have both lengths of the skewer. My best guess is that the length refers to the length of the 5mm section of the skewer, from the shoulder just inside the lever housing to the end of the thread.
The longer version was just long enough to fully engage the threads in the metal part of the nut. It doesn’t quite thread all the way through the plastic part, so I guess it’s not quite acting like a nutloc. It will be strong enough to put the full tension through the skewer though, I guess there’s just a small chance of it coming un-done.