> I don’t know in which air-sphere (tropo etc.) this flux is taking place

That figure seems to be the daily variation (0-24) in carbon dioxide due to uptake (blue) or release. I expect it's only the lower part of the boundary layer (which is itself the lower part of the troposphere). Then the shifting pattern in the figure would have nothing to do with winds, it's just because the sun is moving from east to west and plants react to that (perhaps factories too ;-))

[Added: if I remember correctly the well-mixed refers to the stratosphere, where the carbon dioxide influences the radiative forcing]