the witches are implied to be part of the shadowmaster hierarchy, but what the shadowmasters are is never really said. It's possible that the star god species had a divergence along gendered lines at some point after they advanced there bio tech past requiring both genders to viably reproduce.
I think it unlikely the witches are of the species though, more likely just the most potent mystic practitioners on earth, with more then a little legend blur. If they where in fact truely significant personas to the shadowmasters who have been wageing a conflict with the stargods on a galactic scale, why are several of them on an insignificant backwater possession of the Empire more or less twiddling there thumbs when it comes to the conflict? Some of them for perhaps centuries, if you take the descriptions given at face value.
Given what The Well Wisher, and Purple Bloom(Far more likely candidates for actual Shadowmasters imo) can arrange when motivated to do so, implies a higher order of power then what the coven seem to be able to exercise. However the cloak and dagger nature, and the shadowmasters extra dimensional prowess does make for an intentionally hard group to define and identify.