I've just had another thought to do with the design of the vault.
Remember in FO3 when we go back to vault 101 during "trouble on the homefront"? The schematic behind the previously locked picture frame is now made available to us, depending of course on our stats. In vault 111, we know that at least one scientist didn't make it, due to the skeleton next to the vault door controls in the gameplay footage, and there is a fair chance that he was the only one. We also know that this was one of the last vaults to be built. Given the possible 'submarine' based design as I have suggested, what if there was not one but two ways out of the vault. The main one, as well as an escape route for the scientists in case the lift-shaft were to become blocked or damaged. This is how I would picture it:
We leave the vault after completing the tutorial, but somewhere on the lowest level is a securely locked hatch. Some time later, when we've levelled up a bit, we return to the vault, and kill a group of raiders that have since moved in. We then unlock the hatch, and it leads down to a hidden area containing a number of cool items, as well as a submersible. We enter the submersible, and via a large submerged tunnel we end up in the lake north-east of the vault as seen in http://i.imgur.com/tFek3MP.jpg image. The submersible could then be air-lifted out of the lake by vertibird, which would open up a whole possible new area of underwater exploration. Incidentally, the real world lake is actually known as 'Fresh Pond', and is located fairly close to a research facility as seen http://www.freshpond.org, who seem to specialize in evolution and genetics!
To back up this theory, I have posted two new links to the concept art in http://www.gamesas.com/topic/1524192-more-clues-in-the-concept-art thread, showing what would appear to be a small submersible, and also what looks like a giant squid...
EDIT: the hatch leading below the vault could even explain how the Institute gained access in the first place in order to remove our spouse and child.