No, the mpg numbers do not prove the machine knows how to shift better than you do. It just shows that Toyota/Subaru are clever and programmed it to behave in a way that gets good numbers in a controlled test
You could get better mpg with the manual if you know what you're doing. Computers are dumb :P
Also the gearbox is not remotely related to the ISF, it's just got sporty programming. Same philosophy though. The manual gearbox has slightly closer gear ratios than the auto, and 6th gear ends up much shorter, which is why there's a highway mpg difference.
By the way, everyone knew this already, and we've had a lot of threads on it.