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The file contains a binary OLE object Composite Document File (./xl/embeddings/oleObject1.bin) that again contains the PDF. The OOXML markup-compatibility elements for this are <mc:AlternateContent ...> and <mc:Choice Requires="x14"> which Calc doesn't support, so the <mc:Fallback>'s PDF icon is shown.

If you have Excel 2013 or newer you can try to save in Excel as ODF .ods file, but I doubt that will give a usable result.

The alternative could be to not embed the file but link it (as hyperlink cell content or using the HYPERLINK spreadsheet function) instead, residing in the same directory as the spreadsheet file and zip both files together.