Well, if the black smoke monster is Cerberus the security system, (whether or not it is malfunctioning) perhaps it was meant to make sure the volunteers don't unwittingly stuble across the "?" in the centre of the island. It makes sense that there would be measures in place to protect the experiment.
The black smoke monster might also be part of an observation system, a la "remote viewing station". That explains why the "dark territory" is closest to the area of the RVS on the hatch map...