I'm guessing that the plugin isn't going to handle that particular metadata correctly because your source isn't valid EPUB2 to begin with. The "media:" prefix (for media overlays) is not part of the ePub2 spec to my knowledge. It's ePub3 only.
ePub3-itizer converts ePub2 to ePub3 ... not ePub3-ish to all the way ePub3.
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