I apologize in advance for the long text. With the Aretuza Journey nearly coming to an end now, I though that no other time would be more appropriate to discuss such matters.
Witches are indeed real and pose an actual threat in the Witcher universe. However, instead of being simple female mages and sorceresses, real witches are a sort of race or species that seems to have an appetite for human flesh (namely that of children).
We don't know for certain how witches come to be. Are they born? Are they made? Were they once human and were then turned into witches? We know for a fact that the Crones were made by She Who Knows mixing her blood with mud and bringing them to life through the use of magic (a resource that came into the Continent only after the Conjunction of the Spheres). But the fact that witch apprentices exist (and that they looks particularly human) might suggest that most were actually human at some point.
In her scrolls, we learn that She Who Knows is an unimaginably ancient pre-Conjunction creature and that she is also described as a sort of witch. Yet, it is said that "even though many new beings had come from the Conjunction, there were still none like herself", which means that (besides the Crones), no other witch existed in the Continent or came into it from another world. We know for a fact that every witch we know of other than She Who Knows cannot have lived there before the Conjunction, as they always appear next to human children (and humans are also "post-Conjunction creatures"), and thus we can only deduce one of two things: either She Who Knows or the Crones created more witches (or turned human girls into witches), or the witches we know of are not from the Continent and they simply belong to another universe that never came into contact with the Continent. For the sake of continuity, the first option seems more likely.
We know that, during the Sabbath in Velen, young men and women that go to the Crones as "gifts" supposedly come back feeling blessed and usually just leave their homes to live a happy life somewhere else. We also know that this is just a ruse and that those people are just simply eaten by the Crones, but it is also possible that either some of the girls are bewitched and taken as apprentices or that the Crones create new witches from mud (like their mother created them) in the likeness of the ones they have eaten. (The "Witches' Sabbath" card seems to allude to this event of either turning human girls into witches or creating new witches that will learn the ways of their kin.)
Whatever the process, we know that there are more witches somewhere, and that they have a structured hierarchy. Yaga is the Queen Witch, whom the others ultimately serve and to whom they give bewitched children as offerings for her to feast upon. Mammuna and the Rat Catcheress seem to be sort of the "higher witch" type, and they appear to be bewitching children either to eat them themselves or to bring them to Yaga as offerings. Then there are the lesser witches, who seem to be doing the same sort of kidnapping as the "higher" witches, though they are most likely less ancient and less powerful than witches like Mammuna. And finally there are the witch apprentices: those who have been either created or "converted" recently (probably after the Sabbath) and that are just now learning of the witches' magic and ways, and whose bodies still seem to remain intact (in opposition to the deformed bodies of fully fedgled witches).
Gernichora is and entirely different case. Her chest reads: "Gernichora was, in fact, a post-Conjunction monster whose name derives from the Elder Speech. The elves called her Gvaern Ichaer – the Bloody Mistress. The Aen Seidhe, though incapable of defeating Gernichora, did their best to limit her power. When the last elves left Angren, their warnings fell on deaf ears. It wasn't long before the effects of local ignorance and negligance were felt…" It is possible that her more human-like form is the way she was left after the elves "limited her power". We know that she used her blood to control the monsters of Ysgith by giving them her "fruits" (which are simply leeches filled with her blood); and, therefore, it is possible that the effigies she is placing on the trees could just be magical ornaments created by her that have a similar effect (if they manipulated humans or monsters, we know not). Whatever the case, it appears that, after some time, due to human neglect (and possibly her machinations), she regained most of her previous power and became once again a powerful creature. Perhaps she was aided or taught by the witches (explaining how she could make the effigies and her card's Sabbath mechanic)? But what would they have to gain? Perhaps she too eventually lead wayward children to Yaga as part of some bargain. Or perhaps none of this happened and she simply knew magic already (maybe even before coming to this world). Whatever the case, Gernichora is NOT a witch, even though she may have ties to the witches. She is simply an incredibly rare specimen that came from another world (possibly even the only one of her species).
As for the other relicts of the expansion, not much needs to be said. Relicts are simply creatures/species that once were abundant and are now rare. Witches are rare, if any still exist at all by Geralt's time (other than the Crones, of course). And, like witches, so are selfeaters (not much to wander as to why they are unlikely to survive over time…), gan ceann (a creature you would already know of if you are familiar with Irish legends… or if you have watched "Durarara"…) and incubi (the male version of the succubi).
I hope some of you have found this interesting. I encourage you all to share your own thoughts, speculations and theories (even if they conflict with mine)!