Correlation Not Causation
Niners are most efficient team as scoring points per yards gained (1 point for every 10.87 yards gained). Additionally, they are most efficient at not allowing points per yards gained on defense (20.76).
The statistics suggest the Niners get better field position than their opponents (the product of good special teams and turnovers) and they score more points and allow fewer in the red zone. Now - I'm not sure what the stat means - either the Niners have been lucky or good. Either way, the stat alone isn't necessary the cause of winning and success, it could be the other way around as well - successful teams will tend to get better field position and score in the red zone. So anyway, it is a correlation/causation thing.
UPDATE: A WSJ piece on Delanie Walker, the 49ers utility guy on offense.