Sam, some AOA indicator systems (all of the big boys, military stuff, the executive jets, etc. and a few small GA experimental systems) take into account flap settings, because it does matter. Most of the GA types, such as the one on my plane (Alpha Systems AOA System Enhanced Classic 4" Horizontal Display, pictures are
here, above the ADI), do not. Instead, it is calibrated with the aircraft clean, at Vs, Minimum controllable flight, and a few other speeds. Here's what mine looks like, and what the lights signify:
Today, on base and final I went as slow as I could without going below the 8th light. The AOA indicator is just below my visor and in my peripheral vision. I can do this no matter the fuel, cargo load, or bank angle, and not stall. I am conditioned to push forward when the lights start to go to the left. In an emergency, I can fly a true "Best Glide" regardless of payload, or any other factor just by keeping the 10th light lit. I can climb out like a batoutahell by rotating when the red lights turn to blue and by maintaining the climb with the 8th LED lit. All, regardless of weight or bank angle.
A "Ding Dong" "Getting Slow" comes through the com system if speed is below 8, followed by a "Too Slow" announcement when below the 7th LED.
With any amount of flaps extended, you have a safety margin above and beyond the clean configuration so I don't really need (or would want) to have flap position factored in.
An airspeed indicator cannot do any of this for you.
This system cost me ~ $1,000 and I did the install myself, with a logbook entry only, signed off by an A&P friend.