Is it possible to customize the splash screen on Windows to not display the quality selection? Or, to change the background color of the control UI.
If you’re talking about the screen that appears in the standalone player where you can select resolution and customize inputs, the settings for that can be changed by going to Build Settings → Player Settings → Resolution and Presentation.
Here is the link to the docs for that:
http://docs.unity3d.com/Documentation/Manual/class-PlayerSettings.html