cPanel 11.25.0-R46156 - WHM 11.25.0 - X 3.9

In Feature Manager -> Disabled Feature List unchecked boxes are the disabled features. Those (should) appear greyed out in other feature lists. However some features appear as normal (selectable) checkboxes in Default Feature List (and other custom lists) even if they are disabled (i.e. not selected) in Disabled Feature List. This allows disabled features to be added to the feature lists.

See this screen capture of the Default Feature List for an example.