Shouldn't the upwash on an airfoil increase the effective angle of attack?
The problem is the true AOA varies depending on where in the flow you measure it.  So what point do you use?  An inch forward of the LE?  Farther forward?  Higher? Lower?  

Better to use a consistent value that is independent of the local flow variations in the upwash by using the angle of the chord line to the free stream.