The story doesn't really make sense as told. It fit's Quirrell's view of the world to a T, tough, so he isn't questioning it enough.

Dons tinfoil

Someone on reddit pointed out that "confused scribble" might simply mean "A busload of aurors in a bag of holding" Now for really amusing wtfry, let's make that "A busload of arch-wizards."

Follow me down the rabbithole for a second: Voldemort's read on the tale of Perenelle is obviously, blatantly, just wrong. It fits his worldview far to well, and has some logical flaws in it, especially concerning the cup.

So, I had a thought. As Harry pointed out, one thing to do with immortality, is to share it.

Further, it is a core part of wizarding culture to not share dangerous magic freely. And the stone is dangerous. It isn't just immortality, it is also a weapon of utterly insane destructive potential.

Theory 1: Baba Yaga is not dead. Perenelle was simply the first person she chose to share her secret with. I give this one quite high odds. The most likely alternative is that her death was accidental, which would be just.. ugh. Traumatic, much?

Theory 2: All those historical wizards that lived very long lives? Those were her further apprentices as she - being appropriately cautious with the dooms-day device - established that they could, in fact, be trusted with this level of power over a very long period of time. (.. and probably some mind-reading) Most of them are also not dead. And most of them are sitting in that chamber, playing poker.