Yes i agree, it doesn't make sense but probably it's gear ratios are adjusted in lower range. I've another manual and a cruisetonic around me and have driven and inquired from their owners. As per my driving style, Cruisetonic shifts gear at 2500 RPM. In 6 Speed, I shift upwards at 2000 RPM. So lets say, if accelerating upto 80 kmph by keeping the driving style and engine capacity constant, a 1.6 manual 6 Speed will achieve it at lesser RPM range. So talking solely from fuel consumption point of view upto 80 kmph, Manual version has an advantage.
My vehicles fuel average is calculated on Salam Interchange to Salt range patch. On uphill drive towards Salt range, average is15 km/l, on way back (downhill patch), average is 15.5 - 16 at most . Motor Oil being used is 20W-50 (bcz previous owner maintained so). Fuel averages of vehicles mentioned above are almost the same. Cruisetonic owner states that he gets this average at 110-120 kmph speed. I easily achieve 650 km in one tank full.