Although you are right, it seems like the ports module won't line up correctly in many of the different standard AT cases. I had to machine a panel for the ports module and dremel out a section on the case. Not perfect, but it's good enough.
Let me know if you find a source for the correct Enlight or Quikpak/Amiga Tech cases. I have an A4000T without a proper home also.
Good Luck,
Jeff