Ninja Gaiden 3: Razor's Edge [BLJM61010]

Discolor Cutscenes (Res. Upscaling)
# Enable Stretch To Display Area (GPU)
# Set Res. Scale Threshold = 1024 x 1024  (GPU)

Why are you recommending people use stretch to display area? All that does is stretch the image, which is obviously awful.
Also, 1024x1024 scale threshold will make resolution scaling look worse. Only 580x580 is needed for this game.

Stretch to Display Area is not needed, and will only make it look horrible on non 16:9 monitors / when windowed with different aspect ratio's

Performs very well with me when upscaling.  You can check the attached comparative picture, which I also included in your suggested setting.  It appears your suggested Threshold Value works very well, too.  Really Helpful suggestion!! 
Good thing that you pointed out about screen ratio since I’m only dealing with a 16:9 ratio.

Btw, how did you figure out 580 value is well-suited for Res. Scale Threshold. 
As you know, some playable games-titles requires a different set of value when upscaling (such as Yaiba: Ninja Gaiden Z & Remember Me ... so on).  I usually follow the method of assuming the power of 2^n (256/512/1024) and luckily ended-up with well-rendered/performance.