Modifying the EEPROM is no more difficult than modifying the FLASH. You can prepare a HEX file for the EEPROM contents, and program it with avrdude, exactly as you can for the FLASH. It is also trivial to provide a Serial interface function to accept EEPROM data, and write the EEPROM. It would be equally trivial to only allow that function to write to a fully erased EEPROM, so that one written the EEPROM contents could not be modified again by the same mechanism. Trying to put FLASH data at a specific address is about the worst approach to take, and unnecessarily complicated.