When Apple acquired Beats, it was thought they wanted their efficient manufacturing techniques for different combinations of styles/materials. The customization of the Apple Watch bears this out.

It seems reasonable they might next apply this to the iPhone - and it seems the different battery sizes you suggest would be easily accommodated. (Unless there's another reason they want to constrain battery sizes).

EDIT just thinking of Christiansen's ideas on evolution of products, basically from "integrated for performance" to "componentized for customization", it does seem that iPhones are now overpowered for... well... phones (they are pretty much last-gen console/low end PC level now, or will be soon). Therefore, people might soon stop being willing to pay for even more performance (maybe). This is a problem for Apple, because they don't like commoditized products, not from a margin point of view, not from a building cool new stuff point of view. A way out of this is cool designed customization - it's something that Apple likes, and has great margins (like Beats).