Generally speaking, while calculating fuel economy, tuning is NOT the only important thing. Certain other variables also play important roles when it comes to calculating fuel economy.
Rule of Thumb: Keep it as much STOCK/manufacturer recommended as possible.
Particularly ask yourself how close or far your car is on the following from STOCK specs/Owner Manual recommendations:
1) Tyre size
2) Tyre air pressure
3) over-all health of tyre (tread wear etc)
4) spark plugs/wires
5) Engine oil grade.
6) Oil drain interval
6) air filter
7) Transmission oil
8) quality of fuel.
9) driving style. (steady acceleration/light foot/raving/gear selection etc)
9) cooling system with or without Thermostat valve ??
10) Radiator fan automatic or direct ?
11) Wheel alignment/balancing.
12) Load capacity. (single/two persons~ 5 persons or more, roof rack etc)
13) Load management (distribute load evenly or not)
14) aerodynamics (tempered or not...such as roof rack, non OEM spoilers,sun/rain visors etc)
....and the list goes on.
Individually all these have a minor/major impact on fuel economy depending on case to case.
PS: Vitz 1000 cc is a 3 cylinder car. 10~13 km/liter is a reasonable average one can get from it.
Vitz 1300 cc (4 cylinders) has a better response and economy on petrol. Enjoyable indeed.
Avoid CNG on a JDM A/T.