This setting controls NCrunch's behaviour when trying to render code coverage markers that are invisible (or near invisible) against Visual Studio's background colour.
When the setting is enabled, NCrunch will automatically reverse the colour of any markers that clash with the Visual Studio background. When the setting is disabled, NCrunch will render the markers according to their colour configuration and will not consider the Visual Studio background colour.
This setting is useful because it allows you to easily switch colour schemes inside Visual Studio without needing to manually adjust your marker colours.
It is impossible to make any markers completely hidden with this setting enabled.