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Yes your plan looks fine to me. You can boot from USB for the first time and then program the EEPROM with the new firmware.
Either NOR flash or I2C EEPROm both are fine for storing the firmware image. The difference lies in erasing, EEPROM can be erased bytewise but flash memory can be erased only block wise. If it is fine for you then its your choice.
Thanks & Regards
Thanks Abhinav for reply.
I noted your point.