I thought Baron Fairrow (Pharoah) was in charge of the Academy. He is confirmed by the tooltips to be running the Snowmoors, and the whole story with Jefferson (Joseph) takes place in the Snowmoors, and Joseph's story took place in Egypt, or at least a large part of it, anyway.
It's a little fuzzy because there are references to Joseph's brothers and the "pit" story also takes place in the Snowmoors, in addition to Victoria "throwing him in jail" which is Potiphar's wife, but then the player gets him out. Then we have all the science experiments until we get the Snowmoors Great Engine started.
Episode 3 actually seems to leave off in the middle of Joseph's story. I think that would have to be finished before we get to the Exodus - I think we will see Jefferson and Fairrow meet eventually on good terms. headscratch
The Fogworks seems to be an analogy for, uh, hell. Nobody who goes to the Fogworks ever comes back, and the only thing that comes out of it is automations and heartbreak. Sounds like hell to me.