Not sure if this was answered yet. But I don't feel like reading through 10 pages of speculations. My apologizes.
Emu scaling doesn't work right now because XC3's engine uses a new Temporal 2x Upscaler. The game renders natively at 360p handheld, 540p docked. With the new scaler it outputs at 720p/1080p
Anyone using a lib_nx engine mod that has working emulator scaling is using ColReduction false.
ColReduction false disables 100's of shader effects and breaks the Temporal Scaler. It is also the reason why in game cutscenes look lower res than in game play at times. Has nothing to do with the 238 pre rendered vp9 .webm cutscenes.
Any resolution value over 2.5 will automatically default to 2.5
Turning blur2, blur2hlv, or furblur off will also break in game cutscenes.
I am still testing and trying to get values labeled for the lib_nx Engine mod.
There are mods being tested that will remove the scaler properly, one for 1440p native resolution among other things that should be ready in a week