Baba Yaga has “been dead for six hundred years,” and a quick Wikipedia search suggests the historical myth is first recorded in 1755, nor can I find anything particularly relating her to being from around ~1400. Nicholas Flamel is six centuries old (canonically, he was born in 1327), which means the Philosopher’s Stone, if it exists, is around the same age.
Not sure what kind of coherent theory you can come up with to put it all together, though… Voldemort = Baba Yaga seems a little… silly, especially given Quirrell talking about female wizard rapists, which, given that Canon!Voldemort is a rape baby and Quirrell is Voldemort, seems like pretty good evidence that HPMOR!Voldemort is a rape baby too.
Maybe Baba Yaga is Nicholas Flamel’s true identity.
From chapter 85:
Did anyone else get this ref? I haven’t seen anyone else post about it.