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In complete agreement with DiapDealer here. Nothing should be storing things (especially unmanifested things) inside the epub's zip folder.
Have you tried simply importing your files into iTunes first just to create those non-spec files for you and then exporting then from iTunes into the Cloud or Files.app for overflow storage?
A better solution would be to File a bug report with Apple to ask it to follow the spec and manifest any additions properly in the opf.
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