When they're talking about the bonkers "Blaaack Flaaag" animus framing device, Sean says "I totally wish I didn't have an NDA, I have a story about this... that would have been amazing if they made the game." And then yesterday, this was announced:
http://www.polygon.com/2013/12/10/5197342/double-fine-cryptically-announces-new-puzzle-game-hack-n-slash
Hack 'n' Slash features a young elf who "uses her computer hacking skills to cheat her way through a classic action/adventure game,"
Seems like a vaguely similar concept, and it came out of one of DF's Amnesia Fortnights, so it's plausible he would have known about it.
Another funny coincidence related to the podcast is that as the guys suggested, the game is pushing this device front and center, using it mechanically as well (and I suppose not at all as an actual framing device) but in any case aren't setting it up and then dropping it on the floor.
Anyway, yay for giving a concept the depth it deserves, and it will be really interesting to see where they take it.
Edit: Sorry for derailing the spoiler discussion