I don't know if any of you have seen Rooster Teeth's Red vs. Blue, but I thought about something with the zombies. It's pure speculation, but I think that our whole conclusion that "Zombies was a lie!" is not necessarily true. Samantha said "...and from that day forward, [they knew] I would protect them". This suggests she had contact with the Original Cast.
Where Red vs. Blue ties in is that (SPOILER) Epsilon (Church) gets trapped inside an AI, and creates his own world based on his memories within it. This way he lives out his life in a happy way.
Samantha is in a similar predicament, and the cutscene may have been her imagined reality, where Richtofen is a playmate and her dog is non-Hellhound-ified. However, based on the Griffin Station logs, she could have known that her father is going to help her out. Therefore, she created a character of her father, remembering his "plan".
The question is, is this while she's in the Aether or in Agartha?'
EDIT - Origins stuff shows Samantha calling from Agartha. Samantha called back in time perhaps? The cutscene is her in Argatha?