So, why not put the playlist file into the same 'book' as the ebook, then you will have the playlist and the ebook file(s) in the same place. A calibre 'book' can have many 'format' files (EPUB, M3U, MOBI, MP4, etc), but only one of each type.
Simplest way to add a file to an existing book is to drag/drop it into the Book Detail panel.
You could listen to a book either by using the View->View specific format and selecting the M3U file, or by giving the M3U/media player combo a keyboard short cut via calibre's built in Open With feature - I use Shift+L.
BR
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