Yes, parts of your theory, and some subjects in the Fallout lore, are to me, not always necessarily confined to just "a game" but a lot of "wild ideas" have their origin in actual life, or atleast information that came from "real life".
The abyss was also a great movie, and the ocean is such a huge unexplored place, I know that the ones who have gone deepest and is most familiar with it, is not the biologists on discovery channel, but the military. Just as the space program happened to be all "military" and then gradually they've become known as something of the civilian society, and that the military doesnt even have a space program, despite that the tech we use we got from the military, all the first astronauts were military, and even today NRO and such give their old equipment to the public, and we list it as the "best", like those two telescopes NASA got back in 2012 https://en.wikipedia.org/wiki/2012_National_Reconnaissance_Office_space_telescope_donation_to_NASA , superior to the Hubble telescope, capable of 200 times (says only 100) the wider view, NASA is still trying to fund money from the public to put them to use.
If the military have telescopes "100 times better" than Hubble, which the mother of all telescopes, and they say that those telescopes are their old outdated ones, then only the mind of a chat-bot would not be able to figure out that they have a very advanced spaceprogram, and it is as classified and unknown as those telescopes were before the military decided to give them to "us".
Sorry for maybe going totally out of topic again, but I do find this thread extremely interesting, and it's 4 more months until Fallout 4 is out, so until I get some more F4 material to chew on, I will most likely let my thoughts wander off to the far of edges of related topics sometimes.
To me the whole MIT-society in the fallout universe is kind of the "classified" secret society of the military, that most people know about, but dont really think or atleast talk that much about.