In some cases, namely the Macinabox VM, the configuration in the GUI may and will destroy entries in the underlying XML, the two ways are incompatible. Many users have fallen into this trap, the impact is not low.   The best solution would be to have the GUI only touch the sections in the XML that it is asked for. If that is not possible, maybe the next best solution is to have a switch where the config GUI can be completely disabled by the author so that only the XML editor