It is exactly because of this problem that Desktop metadata system is designed the way it is. ArcGIS 10.x for Desktop is designed to create and manage metadata that is in the ArcGIS metadata format. All metadata is stored in the same internal format. You edit all metadata content with the same editor and the same user experience, except the specific set of content and validation rules you're working with are tailored to the metadata standard you are working towards as determined by your metadata style. With the FGDC CSDGM Metadata style, when you export metadata to a standard XML format, you get a CSDGM-formatted XML document. With the North American Profile of ISO 19115 2003 (NAP) metadata style, when you export metadata to a standard XML format, you get an NAP-formatted XML document.
If your metadata XML file is in the ArcGIS metadata format, you can export it to the North American Profile (NAP) metadata style simply by choosing the NAP metadata style instead of the CSDGM metadata style in the Options dialog box. Then, use the Export button in the Description tab to transform your content to the NAP XML format.