Always avoid tuning (throttle body cleaning etc.) unless and until your car is giving some problem to you.
The reason for avoiding is that these Cars do not require regular tuning, and the major reason is that mechancs here will ruin your car while messing with it.
Also these complex cars requires re-configuration (calibration) of sensors once they got removed and installed again. (injectors, throttle body etc)
According to my knowledge Passo doesnot require configuration for throttle body, but you should take care from now onwards. Even toyota delaership mechanics do not have sufficient knowledge about these cars.
According to the steps performed by toyota (misfire etc) , and if the issue is resolved now, then i guess when your local mechanic cleaned the spark plugs, there was some dirt etc. remained in one plug.