1. They became unwithered because they were fixed and the Freddy Fazbear's Pizza brand was reorganized and resulted in the pizzeria we monitor in FNAF 1 - according to the newspapers, it didn't close because of the murders - it closed because after what happened in the previous location, no one wanted to go there.
2. Scott originaly went for Dream Theory, but now he said that 'what's in the box has changed over the years'. Originally the box could contain a bunch of toys but now it likely contains C.C's corpse.
3. I think that the theory most relevant right now is that FNAF 1-4 and FNAF 6 are in-universe video games. Ughhh