I don't know, I'm really torn about where Zoe is, exactly. After the events of Book Three, I've looked closer at the ending of Book Two and something weird occurred to me.
Take a look at these two screenshots, one immediately after the blast and one in the scene afterwards, of Zoe in the hospital bed:
Notice how, in the first picture, Zoe is wounded badly. She's bruised and bloody, and from Book Three, we know she had burns severe enough to require skin grafts.
But in the second picture, she isn't wounded at all. Presumably the dirt and blood would be cleaned up so she wouldn't look as bad as the first screenshot, but wouldn't you expect there to be some wounds? She doesn't look burned at all, and her hairstyle is the exact same as the way it was in her comatose Storytime state.
I'm not sure I have a perfect answer, but it really feels like, at the very least, Zoe's body is not in the Stark we've explored. At the beginning of the game, Zoe said she couldn't manipulate real world objects so how did she manipulate that machine and her physical body to wake herself up? Not to mention people telling her to wake up: Zelenka, and twice now Queenie... It just makes me wonder, is this Stark or is this a dream version of Stark? I don't know, it's all quite mysterious.