As for me the masthead is a part of the header but most of the developers consider both as one. However, as for the structural data element concern, I will strongly recommend to add them with in your code, because the search engine are reading them quite efficiently and effectively, however, the time is not far when the browsers, mobile and tablet will start reading them and they will become a standard ranking factor in search engine as well as industry standard. BTW nice and very informative write-up.