Was due to the fact that the instances don't have a "static" obmat that can be referenced to use as a uniform.
Solution : precompute the full matrix for each bone and pass it as instance data. (theses are copied into a buffer and can be discarded right away)
Note: this could be optimized further and make only one drawcall (shgroup) to draw all bone instance of one type (vs. one call per armature).
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