Still not sure of the logic of the tesseract, but the flaws are imported from the original dungeon. How are the rooms different shapes? why are there 48 of them?
Well thanks. that finally makes sense.Note the illustration of the tesseract "unfolded" into eight purple cubes. One room lies on each face of each cube.
The tesseract construction can easily be hand-waved by telling players it's "extraplanar" or "magical."