Where did it go and well on the topic where’d the beanstalk factory and go? Also what is hiding in the hunted manor in the old rooms other then the attic and what’s hidden in the madder horn’s remains?
It's unknown. I believe from what I've read that EM2 had time limitations. I would have liked to see Gremlin Village in it (that's my favorite world in EM) but sadly the developers left it out.
Hard to say whether or not Wonderland and the Beanstalk factory are canon since the Wasteland model from the first game cutscene wasn't technically the final design (As places like Lonesome Manor and Ostown were no where to be seen).