I have a feeling whoever was in charge of achievements and modding compatibility simply didn't think things through. You don't advertise a game as being mod friendly and then block some of the meta aspects behind a wall if you use mods. I am sure it is the product of either carelessness or a poorly conceived of idea that will quickly change once confronted.
Presuming the devs take a peak at this forum still, I think they'll change it eventually. But hey, first make the actual parts of the game like companion quests work, right?
