So according to the game, the Crystal Tower appeared after the Calamity. But the researchers in the area believe the tower was built by the Allagans, meaning they have reason to assume it has been there for eons. At one point, a researcher mentions underground. And while it stands to reason that a lot was unearthed right around Cartenau, it doesn't make any sense that a structure that dwarfs Midgardsormr (which was fully exposed before the calamity) was just under some rock.