Prior to working on lightning I designed electronics and ran a pick and place machine for a small EE company. We could produce thousands of PCBs per day on one line (solder stencil + pick & place + reflow oven) though the average run was much smaller. We did the same basic operations as described in this article - populate PCBs, flash with firmware, package them, and test. Pretty much all of these steps can be made much more efficient if you have the volume to justify it. My takeaway was that it's really a numbers game.

I can't imagine they sell that many $2,000 underspecced phones, but I'm sure if they did, they could find further efficiencies in chip procurement costs, assembly, testing, even shipping. And that's not to mention amortizing the engineering and design costs over a large number of goods sold.