Hmm ok it is just looking at the mods I downloaded from the Nexus just to get an idea of what others are doing it seems that they only include the xml files they need and delete the rest as well as the entries in the submodule, they also change the names of the files by adding a reference to their module such as weapon_descriptions_modnamehere.xml or something which they then update in the submodule to reference that specific file.
That said I placed entries in the submodule to load crafting_pieces.xml, crafting_templates.xml and weapon_descriptions.xml into my submodule (did not change the file names, left them default) and now I am getting the error "Could not load merged xml file correctly: ItemsError: Object reference not set to an instance of an object" and have no idea what this is referring to.