Steps to reproduce:

1. Create a new Unity project
2. Go to 'Player Settings' and make sure the Direct3D9 is used as a Graphics API
3. Build and run the project in fullscreen using non-native screen resolution
4. Notice that the game is "Fitted", that is the black lines are used to keep the aspect ratio correct (best seen while splash screen animation is playing if the project is empty)
5. Change the Graphics API to be Direct3D11 in the 'Player Settings'
6. Build and run the project in fullscreen using non-native screen resolution
5. Notice that the game is "Streched" and does not maintain the aspect ratio (as in step 4, best observed while splash screen animation is playing)

Resolution:
This is related to GPU scaling in AMD's or NVIDIA's control panels.
If GPU Scaling is ON - d3d9 will letterbox, while d3d11 won't - we can't seem to find a way to properly letterbox d3d11.