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If you use the GUI to do conversion, then you have to live with the file/folder structure that Calibre uses to store books in it's library, and there is no way to change that If using the GUI, then you are also expected to use that to export any files from the Calibre library so that the internal storage is then invisible to you.
If you use the Calibre command line tools to do the conversion, then you have explicit control over the placement of files.
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