Exactly, this is why understanding fluid dynamics is so difficult. You can't look at some physical laws and assume that the right hand side "causes" the left hand side. They all represent relations and it so happens that the fluid configuration that fulfill all the relations (and that the world adopts) is the one that causes lift. Just trying to talk about cause and effect is a misunderstanding.
My favorite example of this was in the air-data computer I was working on for a fighter trainer. I was just on the software side rather than the aerodynamics, but it was notable that the corrections to angle-of-attack and angle-of-sideslip measured by the multifunction probes (which are way up at the nose of the plane) included terms related to the position of the flaps (which are way back at the trailing edges of the wings).
I'm not surprised about the angle-of-attack needing correction. The angle-of-attack is defined as the angle between the average chord (an imaginary line running from the leading edge of the wing to the trailing edge of the wing) and the relative wind. Since changing the flap position changes the position of the trailing edge, the angle-of-attack will also change.
Usually you draw a line from the trailing edge (which is sharp so unambiguous) to the point on the leading edge that makes the line the longest.
The definition that makes the most sense, though, is to disregard the geometry of the wing and define zero angle of attack as the zero-lift angle, because then lift is proportional to AoA.
