This is my process as of now:
1 - Filter through meshbuffers, set all vertex colours to 0.
2 - Filter through joints, set all vertex colors to the corresponding joint id. If the first component is taken then the second component will be used (and the third and the fourth), this will result in an even split between each bone, a 50/50 (or 33/33/33 or 25/25/25/25) weight distribution (No we are not talking about Toyota MR2s) between the joint transformations.
3 - Recieve vertex color in vertex shader and perform operations based on said vertex color.
Heres a screenshot of a mesh (Set up for rigid animation, that is only one weight per vertex), showing varying light intensities based on joint id, slightly intensified so that the differences are more noticable:
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Expect a working implementation sometime soon

Cheers