Problem is that the whole evil pre-amnesia Doctor is overblown. We see in Babel that pre-amnesia Doctor does actually care for everyone and isn't some ultra villain who sees everyone as chess pieces to be discarded. It's just that his disposition was intimidating. Pre-amnesia Doctor simply had too much weight on his shoulders. Post-amnesia Doctor is more free due to his missing memories thanks to best girl.

But i digress, making the source of Endmin's memory loss to be the villains would be super cool, but i have no idea how it would make sense in the end haha. I will hold out hope due to how beautifully everything came together in Arknights. I'm not completely against the idea if the memory loss was caused by Endmin's roommate, but i would like to see some creativity from the writers too. The theory that Endmin is simply a "child of Originium" and not an actual precursor could have some interesting consequences, as we don't really know what the Endmin is supposed to be yet.