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I'm afraid the assumption of one format type per book record is very deeply baked in calibre and is not going to change. In any case if you have multiple files of a type in a book double clicking can at best open a dialog to choose which file you want.
Instead what you can do is create a new file format called, say ATTACHMENT. Then when the user tries to open such a format it will present a dialog asking which internal file the user wants to see. And if the user tries to add a second file of an existing format it will automatically become the attachment.
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