Doesn't it confuse you that there's a chaos entity out of nowhere that connects to the Witchcraft Goddess that has nothing to do with one of Chthon's aspects? And consider that the elder god is responsible for some of the witches, wouldn't it make sense to tie those together?
No, it doesn't confuse me. Chthon is an elder god, and the Witchcraft goddess and her consort are abstract entities. These are two completely different types of beings, that occupy different realms and serve different functions in the Marvel world.
Elder gods are etheric beings who were born from the planet's life force. They act as progenitors and antecedents for other gods and different types of magic that are endemic their home planet-- in this case, Earth. Abstract entities are, as the name suggests, personifications of universal abstract concepts. In most cases, that applies to the multiverse as a whole, and they usually live somewhere outside of the material world.
To be fair, in Scarlet Witch (2016), Robinson puts all of his focus on witchcraft, and doesn't acknowledge chaos magic as something separate or distinct-- and he neglects to account for Chthon when exploring Wanda's new backstory. So it is odd to encounter this other chaos entity that doesn't seem to correlate to any previously established lore, and I was definitely a little frustrated about that at the time. But if you assume that chaos is a natural force and not necessarily unique to Chthon, it makes sense that it exists, as witchcraft does, on other worlds. The Witchcraft goddess is an abstract representation of witchcraft in all worlds, and her consort represents the intrinsic connection between witchcraft and chaos.
What is that connection? We're told, briefly, in Scarlet Witch #14 that chaos has always been linked to magic, as it abets the "undoing of physical absolutes." More recently, in Contest of Chaos we learned that witches were responsible for binding and stabilizing the Earth's natural chaos magic, implying a more direct link between witchcraft and chaos, which, again, is represented in abstract by these two entities. This parallels Chthon's imprisonment in K'Lay, but we don't know yet if these two events are connected. I would like more clarity on that, and how it relates to Wanda.
So, I think the whole situation is perfectly understandable, but you definitely have to put the pieces together on your own, which is a little annoying, and there are still some loose threads. Hopefully, with Chthon's escape and Amaranth's arrival, Scarlet Witch will do some more worldbuilding for both witchcraft and chaos magic soon!