@ Gundernak
AOA is usually defined as the angle between the upstream freestream velocity and a fixed airframe reference axis. Since wings are often twisted across the span and this twist varies with flight condition it is generally more convenient to use some form of fuselage axis as the datum - very often the fuselage centreline.
A lifting wing induces upwash ahead of itself as well as downwash behind. Any AOA vane mounted ahead of the wing will see the sum of the freestream AOA and the local upwash. One can either calculate or measure this local upwash and subtract the value from the vane output to get a calibrated AOA that meets the chosen definition.
If, keeping the fuselage inclination constant, one lowers the flaps the lift and local upwash will increase. If you then apply the "clean" calibration the meter will read something larger than the actual AOA as defined. Hence the manufacturer's statement - the actual difference will depend on the configuration.