How can you reference critical angle of attack to the aircraft AoA if you are changing the wing AoA with flaps and slats?
The same reason your trend vectors and speed limitations change on your speed tape and altitude (if you fly an EFIS).
"It's all electrons these day my friend." - I forget who said it.
The onboard computers, depending on your aircraft, calculate Critical Angle Of Attack referenced to the fuse centerline, which is referenced to your aircraft configuration.
By the way, you said you fly a HUD without an AOA indicator. Not sure how long you been flying it, but look in the manual, you'll find the AOA of your aircraft is the angle between your Pitch and FPV. If it's not in the manual, ask the CP, when he is wrong, ask an Instructor at your company (preferably, prior military). Then go back to the CP and rub it in his face. :-)