Hello,
It is recommended to set serial download mode when you're testing software, since the device will go to serial download directly so you may update software.
For production it is possible to set Boot mode fixed, be it by fuses or GPIO to the desired boot media (eMMC, SD, NAND, etc.), since boot media would be clean at first boot, the device will go to serial download so it is possible to flash the device.
Best regards,
Aldo.