Of course. As the camber of the wing changes it usually tolerates more AoA. However, the observable AoA by the pilot is less with flaps down than with flaps up, as I stated earlier and with which you disagreed, i.e. as the camber of the wing changes it happens in relation to the fuselage. That causes that you observe that the whole airframe tolerates less AoA with flaps down than with flaps up.
Yes, I missed your "
in relation to the fuselage"
2bighorn: Alpha is generally referenced from the geometric chord as per what Charge (quoted above) and Stoney say. Otherwise you wouldn't be comparing apples to apples and any comparartive discussion becomes meaningless.
Well, in that specific article we talked about, they made distinctive difference between geometric chord line of the
main airfoil and effective chord line (when high lift devices are deployed) to illustrate the difference in pressure at critical AoA. So, I didn't compare apples to oranges, article did.
If you'd go by that article, than effective chord line is equal to geometric chord line of airfoil with no high lift devices deployed. Which is true. After you deploy flaps and airfoil geometry changes (increased camber), you could say that geometric chord line changes (if you measure from flaps trailing edge), or you could made distinction (effective chord line) as they did. Which terminology is right, whether theirs or yours, is matter of semantics.
It doesn't change the fact how Cl and AoA are correlated.