Magda is or was related to Cthon in marvel canon because both Wanda and Pietro were possesed by him at some point because they were the "Children of Magda" bassically children of both magic and science. I can´t see Magda as being evil at along but I can see how Cthon influence was part of Magda´s reasoning to leave her children behind on Wundagore.
But what´s Natalya Maximoff part in all this is still a mystery, we know she "died" in Wundagore killed by "Wanda´s father" but it was obvious she wasn´t telling everything to Wanda and made Agatha promise she would not tell until the "right time", I could see marvel saying that she and Magda are the same person OR they are different people and Magda´s children that she gave birth at Wundagore, who aren not Wanda and Pietro, are around still on another part of the marvel universe but if marvel makes Wanda and Pietro Magneto´s children again then was he the father that killed Natalya? Why would he do that? and what was he doing in Wundagore at that time? he was supposed to be looking for Magda at that point to apologize for scaring her off, he was told Magda died on Wundagore so he made a tombstone on that mountain for her and visits it every year, this was before he became Magneto because he was still trying to live a normal life.
I could see a grieving Max missing Magda, meeting Natalya who looks a lot like her, and falling in love with her but the reason Magda died, the reason Natalya was killed is very much a mystery and Cthon could very well be connected to all this given his wish to get powerful vessels born of magic and science.