But my preferred theory is that Flamel is Baba Yaga, and Voldemort read that story all wrong because he managed to err on the side of excessive cynicism, which is a lot simpler. No murdering took place at all, just an elopement.

Sure. But we have Word of God that suggested that Baba Yaga would not appear in the story again before the bit where Dumbledore said Flamel was dead. Was that "Baba Yaga won't show up again because 'Flamel', who is actually BY, is about to die offscreen" or "Baba Yaga died six hundred years ago, get over it?" Unclear. But I would suggest that, narratively, the defeat of Baba Yaga by sixth-year Perenelle exists as a clue for the plausibility of the defeat of Voldemort by first-year Harry Potter.