In order to tune the factory ECU you would need some means of accessing the maps, I do not think that is easily done and would probably require a reflash of teh stock ECU. Daughterboards or EEPROM emulators are probably the cheapest and best method. These will force the ECU to read the board/emulator maps instead of it’s preprogram stock maps. If something goes really wrong you just remove the daughterboad/emulator and you are back to stock.
Someone correct me if I am wrong