The shape of a commercial airplane wing (twist, sweep, variation in cord and camber along the span, etc.) is very complex. As such it would be quite a trick to define a true "zero AOA" reference. What ever metrics used for such a calculation would undoubtedly be impacted by flap position and wing spanwise droop that is a function of payload/fuel distribution and wing lift loading. AOA as determined from the body mounted vanes (with correction for known local flow distortion) is presented with respect to the fuselage.
As has been mentioned, transport aircraft that are optimized to maximize L/D are designed to fly with a small, positive pitch attitude. To design an airplane to fly with deck angle of exactly zero in cruise would be to leave unrealized performance on the table! Separately, optimization of takeoff, landing, and ground operations usually results in a slightly negative deck angle when taxiing. I strongly doubt that any commercial transport airplane has ever been designed to have exactly zero deck angle either during ground taxi or cruise.