What struck me odd about the area below the hatch is that whatever the series of tunnels is, it used to be above ground (or below the sea). Why else would it have windows? Notice that when Locke pulls back the curtains, the artificial light is out in an area that Desmond (perhaps?) cut out through the window. Odd.

I noticed that there was some sort of alcove when he opened the blinds. I mean, think of the time it would have taken to build that thing underground, and then remake everything above ground look the same, or back to nature. Whoever planted the hatch, must have been on the island for a heck of a long time.

Good point! Welcome to the Lage! :)