You have to configure the settings separately

Eg click DirectX11 in the drop down. Set to Maximum, run the benchmark and you will get the DirectX11 score

Click the DirectX11 in the drop down, set to Maximum (DirectX9) and you will get the DirectX11 score emulating DirectX9 (it actually says this in the drop down for it)

Click the Direct9 dropdown, then set to Maximum to run the benchmark in DirectX9 mode.

These are the only three settings you really should be concerned about. They must be configured separately (DirectX9 and DirectX11) as they run two different game binaries and have different configuration parameters.

Both of your images in the first image are DirectX9 not DirectX11.

Also make sure to run the benchmark at full screen with only one monitor turned on if you want to get the maximum score. If you have multiple monitors, unless they run on their own GPU, they will impact the score.