At first I wondered if the design was meant to have centrifugal gravity, but then I realized that he was merely showing the cross section of the spokes. There's also the matter of the flat segments, which would not be optimal for a spin-gravity design; also, the artificial gravity oriented windows.
I had also wondered about the double pylons, but I think Tin Man has nailed the explantation: the E was rescaled in reference to the station drawing. Just look at the top view of the ship and you'll see the original, smaller, primary hull outline that is in proper scale with the fore-most pylons.
I like the idea of the extra pods being the storage compartments. I'm leaning toward making the ends of them feature large cargo doors. I think the windows on the outside edges of the pods mean there are at least some habitat areas in them as well.
One of the features that is not shown in the drawing, but makes good sense to me, are windows on the insides of the rings. Outward-facing windows would only show deep space, but imagine the views you'd have of the rest of the station through inward facing windows! I'm taking the rounded inner surface as justification for larger, ceiling to floor windows in these areas. Upper decks in each ring would have windows that allow views "up the stack" and lower decks would open "down the stack."