First of all forgive me if I'm way off, I'm by no means an expert on the zombie storyline.
The Legend of Zelda storyline really comes to mind when I think about zombies due to one thing. In OoT, the storyline got split into two. When Link traveled back to warn Zelda of what would happen, it became it's own sort of dimension, while the one that Zelda remained in as an adult stayed intact.
Maybe something like that happened here, and we're actually experiencing two timelines. The one that's being referred to as imagination, and the other that runs through a majority of the maps. Perhaps when you teleport at the end of the Origins EE, that's when it actually splits, or maybe even during Der Riese.
Again just an idea, I'd love to figure out what's actually going on. I like to think Treyarch wouldn't leave us with something as simple as "It's all just two kids playing with dolls".
I also really like the theory about it being both sides of the development team, very interesting. ^.^