Good catch on the cargo doors. Yes, they are an homage to FJ's SFHQ.
As for the windows: Jefferies shows them on the sides of the pods. My take is that the interior of most of each pod is open space with cargo container scaffolding. Work Bees can plug containers into the matrix. Some can be pressurized and linked to corridors (and each other) for access inside them. The exterior walls of the pod thus have habitable rooms. Picture offices along the outer hull, accessible from corridors. Along the interior walls of these corridors would be airlocks that in many cases link up to cargo containers. If you need what is stored in Pod 3/Deck 7/Bay 26 (Feinberg Oscillating Framizams, or perhaps grain for Sherman's Planet), you go to the appropriate airlock and get it. I assume there would be a failsafe to keep you from opening a door without a pressurized container attached to it. At least that is my take on it. YMMV.
I will probably make more of the windows on the pods dark, as this would likely be a more sparsely inhabited part of the station.