They show it getting restored to factory image.
There's a tool for that (many, many of them), both software-based and physical-based tools that can copy out the SysCFG block and write it into a new chunk of flash.
Would be weird in the actual mass production process if the flash would need to be pre-programmed somehow; one DFU process IMO must be able to do everything needed.
Also if there are two flash chips they need to be installed in a certain order. Not sure of the rationale behind that precisely. I doubt it's a hardware difference.