OMG. Wow. I know this video was made a long time ago, but it's not clear that what you need to do is (and I don't know the terminology) have the main part of the armature (yellow outlined) selected when you are moving it around...fine. But when you want to snap to the 3D cursor and have the skinny part with the "top" ball snap to the 3d cursor that you need to/can SELECT THE TOP BALL thingy. I can see in the video now that that is what he does but it's not at all clear and if you just have the armature selected it will just snap to the fatter end. So.... Moral of the story - you can just select the little ball at the top and then you can snap that to the 3D cursor. If you try to MOVE the armature with that little ball selected, though, then move seems to work as scale/shear.
In other words:
You can think of a Bone in Edit Mode as a single Edge; it has two Vertices at the ends. You can move one Vertex ('ball'), or both (the whole Edge) at the same time. Moving one Vertex ('ball') is Scaling and/or Rotating that Edge (Bone).
The big difference is with Snapping; if you Snap an Edge to the 3D Cursor (or to something else), it will collapse that Edge into a single point, whereas Snapping a Bone will Move the Bone, so that its Head (the "big end') is at the snapping point.
Remember there's a fundamentals of rigging for a nice refresher of some rigging knowledge:
https://cgcookie.mavenseed.com/courses/learn-how-to-rig-anything-in-blender-fundamentals-of-rigging
I need to re-watch it, I have to step up my animation in rigging game.