Started new GW campaign, uber, relentless, as purple faction, with Commander loadout, and sub commanders in game have same color, purple, as my commander. Units and structures too, don't know which are mine, which are not. Had a few other GW campaigns, same setup, only blue faction, sub commanders were grey, as it should be.
Boss assistants can be used as sub-commanders, and often have colors assigned. Legonis Machia (blue) has no boss minons, so no colored commanders.
If that is the case, i think that this is not a good thing. It is very difficult to tell apart own or AI units and structures. A slight color variation will remedy this problem.