Looks like a glitch in GhostAuthoringComponentEditor.cs
Around line 156 the new GhostPrefabType settings are initialized with the old ones:
GhostPrefabType newPrefab = prefabType;
A few lines below there is a call into a function ShowPrefabType that draws the GUI toggles. The issue here is that newPrefab is only modified when the option is being toggled on:
if (EditorGUILayout.ToggleLeft("Server", (prefabType & GhostPrefabType.Server) != 0,
GUILayout.ExpandWidth(false), GUILayout.MaxWidth(90)))
newPrefab |= GhostPrefabType.Server;
The end result is that the new prefab settings can only be whatever the previous settings are plus whichever toggles are being enabled.
A workaround for this at the moment is to right click the component in the GhostAuthoringComponent Components list and select “Remove Component”. This will disable all prefab types for this component and allow you to re-enable the ones you’re interested in.