As for Dharma they built on those areas on purpose. Maybe alluding to one thing to the non-crucial personell, but there ultimate goal was to harvest and "exploit" what was on the island. To who's advantage we will know soon enough.
As for Ben, not a fan of the character, but he had help learning things and from the islands own, Richard et al. Ben does what he does for the island, there is no doubt and perhaps even though Dharma's intent was not malicious, overall the "true natives" had a different perception.
Sorry still do not believe this has anything to do with Aliens.
I do believe this is of a "spiritual" nature however one perceives that. Actually I much prefer the calendar theory