...These options are used for all ArcGIS programs. This allows you to save time and display your raster data consistently...
You are changing properties that are at the application level and not at the dataset level. I'm not personally aware of anyway of accessing those unless its some sort of registry access?
in my opinion, this is a problem only in the 10.2.1 version. In the previous versions, every options were correctly saved in the MDX file. I do not think that it depends on which level or somehing similar ...