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As you figured out, when headers and footers are truly embedded into a PDF procedural stream, most PDF utility apps will not physically remove them as this would require parsing and interpreting the PDF stream and figuring out which part of it displays graphics outside the bounding/clipping box and removing those instructions. This is very difficult to do cleanly and reliably. The real issue is that calibre does not correctly pay attention to the PDF clipping box when converting the PDF to EPUB, as it should.
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