Most likely, they weren't looking at the A16 needing to support USB3, since it was a phone chip (iPads now running on Mx chips instead), and Lightning didn't support USB3. The USB-C mandate was only a year ago, and I expect they probably were planning on exactly what goes into the A16 a year further back, so unless they respun a new A16x chip that had the USB3 controller, there's no point where they could have forecast the A16 actually needing to support USB3 until it was too late.