Seperate rig and skeleton?

Hi, I’ve been looking through this about animating custom models for Half-Life 2. It basically says that there is the skeleton which is used to deform the mesh, and the rig, which is used to control the skeleton in the modelling program. Only the skeleton is exported into the game, not the rig.
From what I have read in the docs and things, instead of a rig, null bones tend to be used, which would actually be part of the skeleton.
I’m basically trying to see what I need to do to animate my model. Is there a way to make a rig like described in this doc? Or do you think that nullbones can be used and possibly just shrunk down to a very small size so they don’t create a noticable effect in game?

EDIT: Hmm I was just thinking that bones used as targets for the knees and elbows could be a problem since even shrinking them down they wouldn’t be ‘hidden’ in the main skeleton as they are outside it.