Say you keep the boot pin high on the PCB, then it will always go to the bootloader.
Through USB you can flash everything you need.
Say something went wrong, then no man overboard. The device will keep booting to the bootloader because the boot pin is high.

You've got time to verify the flash went alright. When you've done so, you can change boot address for when the boot pin is high to the address of your firmware.