NuKit allows customization of several Dock settings, which are not available via standard Dock preferences. The settings to change are:
Disable 3D Dock appearance toggles 3D mode to 2D.
Dim hidden applications makes hidden applications icons in Dock transparent.
Show only running applications hides icons of non-running applications from Dock.
Note that Dock settings will take effect after pressing Apply button at bottom panel of NuKit window.