This isn't that relevent to the topic, but I thought I should let you people know there hasn't been any offical word if the house in twilight town is actually the organizations headquarters yet. Although it is possible and one would easily assume that it is because of the screenshots and because you see Diz and one of the Unknowns talking in one of the rooms of the household. But that still doesn't change the fact that there isn't an official word if that building realy is the Unknowns HQ.
In regards to the creators of the dusk and how they came to be. Considering all of the information it is very well possible that the dusk were created by the Org. Sense Marluxia is seen on top of one of the dusk in CoM. This might mean that the dusk very well may be man-made.