Ultimately, the show should have taken the approach that Plagueis/Qimir were behind flaming the conflict between the Jedi and the witches. And Plagueis taught the coven leader how to create a powerful Force being, but she messed it up and the chosen one split into two. They wanted the conflict to happen so that they could take the children and give the Jedi a bad rep. Killing two birds with one stone.

I’m hoping that by completely removing the flashbacks, or perhaps by sprinkling in a couple of brief visions of their mother(s) as idir_hh pointed out (such as when they are arguing about how the Jedi could discover how they made them), that this becomes the most obvious explanation. Especially after the Sith cameo at the end.