Dear Daniel,
I described how x_disk, y_disk, and z_disk are defined in my posted dated Sep 29, 2016 in the forum topic linked above: Azimuth Angle of the Blade.
Yes, I agree that a blade pointing up will have an AeroDyn azimuth angle of -90deg for Case 2 and 90deg for Case 3. Without the Pitt and Peters skewed-wake correction enabled (SkewMod = 1), I would expect the AoA to be the same for this blade orientation because the streamwise (axial) component of the blade velocity is zero. When the skewed-wake correction is enabled (SkewMod = 2), there is a correction to the induction at this blade orientation and the AoAs would then be effected.
I hope that helps.
Best regards,