This is what I have to do as well. Hopefully, there will be fix.I have similar problem. My native monitor resolution is 1920x1200, but I want to play in 1920x1080.
My workaround is to change desktop resolution to non-native (1920x1080) first, then launch a game in full screen mode set to 1920x1080.
It looks like the "full screen" is in fact a broken "windowed full screen" (borderless window stretched on all available desktop area).