@Needlehawk - no, that metadata.opf file you find in your calibre folder is nothing to do with the internal metadata manipulated by this plugin for an epub. That opf file is primarily a *backup* of the data stored in your calibre database for your book, in order to facilitate an emergency restore of your library data should the original metadata.db database become corrupted.
Inside an epub file (if you unzip it) you will find a .opf file which contains the actual metadata used by the epub readers. It is that internal .opf file that this plugin manipulates.
As for removing non DC: metadata, it is an option really only targeted at a small subset of users who are sharing/publishing their epubs externally and require all traces of application specific metadata such as from calibre or Sigil removed.