The answer at last!

The problem of making a joint correction morph (or any other morph) on a posed character is solved! Colorcurvature has made a suite of python scripts which is called Pose Morph Loader.
He was kind enough to let me test this out. After a bit of trouble with Hexagon 2.5 (which contrary to some reports still screws up vert order) which he has now solved by adding a Hex option, I can show you a couple of joint correction morphs.
This is K4 which I have morphed to change the shape from the default (which looks like a dwarf) to a more child like shape. I also changed the Joint Parameters to compensate a bit for that, but there were still significant joint bulge issues. It maybe that I just suck at handling JP's but that aside, I have now been able to make transferable joint correction morphs with the help of Pose Morph Loader. Below are pics of shoulder and knee, before (left) and after (right). Whatever you may think of the morphs (and I admit they need more work), the point is that they look exactly like what I made in Hexagon. Pose Morph Loader works quickly and easily without any tedious messing about with trying to subtract the effects of joint bends and JCMs (which may or may not work anyway).

I understand that Pose Morph Loader will be released soon. I'm sure this will result in some great morphs being made :)

Thanks colorcurvature,

Isaac