The XML tags are actual XML text files which could be embedded into an MKV (or MKA). MKVToolNix can display any existing ones and edit too, but no batch handling. JMkvpropedit (batch capability) primarily can add or replace exisiting Header tags, but can't display them in its own GUI. For example: Title, Date, Name, Language, cover.jpg, attachments, etc. I assume the metadata that you could put and edit in the Header Editor are the Header tags. I can't remember if I was the one who called them Header tags, maybe I got it from someone else or from other sites, but I do call them Header tags myself especially because in the MKVToolNix package, such tags can be edited by MKVToolNix GUI's Header Editor (the Header editor tab). Well I must first admit that I am just a Matroska User as well, so I might be inaccurate. What is Matroska HEADER vs XML tags as not sure I follow and Matroska spec is kind of confusing to try and understand fully. But after re-muxing with MKVToolNix, such issues are gone. I also recommend to re-mux the Matroska (MKV) files using MKVToolNix after editing their tags/covers/attachments (especially Header tags) with JMkvpropedit (since it relies on MKVToolNix's mkvpropedit.exe) and especially MKVToolNix GUI's Header Editor.ДЇor example, the embedded XML tags and covers would not be shown by MediaInfo anymore, and sometimes Avidemux would have difficulty seeking with such edited MKV files. Best tool to connect the UID's of the XML tags (which were added/edited by Mp3tag/chapterEditor earlier) to the multiple embedded covers for example. To individually add/edit/delete/embed or make corrections to covers, attachments, and Header tags (not XML tags). Best tool to connect or correct the UID's of the XML tags and the Chapters. To further add/edit/delete and make corrections to those embedded XML tags (not Header tags). So far Mp3tag can not yet embed or remove existing Matroska covers, but it can display them. Thus no need to create an external XML file from scratch anymore. Conveniently, it would also include XML tags connected to the Chapters if the video has such.

To BATCH add/edit/delete Matroska embedded XML tags (not HEADER tags). To delete existing Header tags, it's more useful to use MKVToolNix GUI's Header Editor (see below).

Note though, JMkvpropedit is more useful to 'add' Header tags. To BATCH add/edit Matroska HEADER tags (not embedded XML tags). JMkvpropedit (uses MKVToolNix's mkvpropedit.exe CLI, and latest v1.4.3 requires JRE up to v10.0.1) Though Matroska I believe has two unique metadata: the quite limited HEADER tags and the apparently unlimited embeddable XML tags.ДЎ. For my many, many Matroska videos (MKV), I use the following below.

Remove mkv metadata