So, I am wondering if Youko isn’t more or less replaying somebody else’s memories when she has these visions of a pre-apocalypse world.

That’s a good point. My current working theory is that the “sister” character is a teacher AI from the shelter MC grew up in. Maybe based on a real-world person like the robot in this episode. The memories/flashbacks are from some sort of future VR learning course. She is always drawn with some sort of digital fringe in those scenes.

Either way, it’s enough of a mystery hook to keep me watching.