ArenMook, if you set the reference atlas to None or null in script and you update the replacement atlas in Awake(), then set the replacement back to null OnDisable(), UIAtlasInspector changes the atlas from a reference type to a normal type.
Put simply, you cannot set your atlas to be null although this could be desireable. Why would you want this to be null? If you are testing the switching of Atlases in the editor from type None, to your switched atlas when you press play in the editor, it will stay the switched type after pressing stop, so OnDisable you set the atlas replacement back to null as a convenience but NGUI detects a null replacement and switches the atlas type from reference to normal.
If you desire this behaviour, comment out these lines in UIAtlasInspector.cs, but it will break the creation of new atlases:
if (mReplacement == null) mType = AtlasType.Normal;
if (mAtlas.replacement != null)