I just rewatched this episode, and something occurred to me. The barracks were built by Dharma, before Ben was on the island. So does that mean that someone in Dharma built the secret room, and the secret secret room, back then?
Otherville was constructed atop the ancient ruins of another culture, one that possible created Smokey. The secret door led to a chamber where rituals were made to the gods of that culture. Smokey is an "extension" of those gods made manifest over many years. The culture thereby gave the island "life" inadvertantly. DHARMA scientists stumbled upon this chamber and decided it was best to keep it hidden from unauthorized eyes, so they hid Smokey's chamber under the barracks of the DHARMA leader. Unfortunately, they did not forsee being wiped out. Ben found the door, translated the symbols and found a way of "resurecting" the ancient power, so to speak. In this light, Jacob is but an extension of another force on the island. So you have one for seemingly good, one for seemingly bad. Light and dark - both raised by the ancient rituals on the island.
The "donkey wheel" is another part of the ancient complex. Again, DHARMA scientists found the site and "buried" it under their own, tapping into the power source of the wheel which they used to temporal experiments. Ben, after completing his coup over DHARMA, read about the ancient "temple" in DHARMA documents and learned what the scientists knew of the "time wheel".
Of course this is just a theory
