Where did you get the impression they were procedurally generated? They all seem very intentional to me.
Well, I just did another two runs and looked at the level map. The levels were different each time.
First run
Second run:
My guess was that they were procedurally generated. It's also possible they might be just random. But I haven't played enough (yet) to confirm either.
They are arranged in a different way at any playthrough, but the levels are man-made. You'll see. :)