At the October factory tour they demonstrated how they can replace the stamping dies in mere minutes. They're on these massive carts that roll on rails. I believe even for the Model S they swap out the dies and do different body panels in batches. There aren't that many stamping machines, after all (certainly not one per body panel). They definitely do not stamp body parts linearly with the production of the vehicles (i.e. stamp out one whole body, then the next body, etc.), but instead they run the different body parts in batches which are then assembled later.
They also showed how the robots can quickly swap out tools from a supply of tools (including arms custom fitted for each panel), so it appeared to me that they've been thinking from the beginning about supporting different car models and I don't think it will be much of a stretch for the assembly line to support it.