Can ALL the fuel and refining equipment be removed from either variant in favor for an all-cargo carrying version?

No, you'll always have internal fuel support systems taking up some space. Think of it this way: on the Hull series, the cargo is fully separate from the ship and the job of the ship is only picking it up and dropping it off. On the Starfarer, the ship has to interface directly with the fuel pods in flight... so there's all sorts of internal plumbing to support this.