Looking at what files and drivers the Facetime.app loads, it loads the SD resolution from the Face Time Camera driver, instead using the HD resolution./System/Library/Frameworks/CoreImage.framework/Versions/A/Resources/ci_kernels.metallib
/private/var/folders/xl/fxfqtrn56kb_hn6s2rcns3p80000gn/C/com.apple.FaceTime/com.apple.FaceTime/com.apple.metal/libraries.maps
/private/var/folders/xl/fxfqtrn56kb_hn6s2rcns3p80000gn/C/com.apple.FaceTime/com.apple.FaceTime/com.apple.metal/libraries.data
/private/var/folders/xl/fxfqtrn56kb_hn6s2rcns3p80000gn/C/com.apple.FaceTime/com.apple.FaceTime/com.apple.metal/Intel(R) Iris(TM) Graphics 6000/functions.maps
/private/var/folders/xl/fxfqtrn56kb_hn6s2rcns3p80000gn/C/com.apple.FaceTime/com.apple.FaceTime/com.apple.metal/Intel(R) Iris(TM) Graphics 6000/functions.data
All other apps on my mac do use the HD output (like Quick Time app).
At this moment I do not know why is it using the wrong resolution for Facetime.app.