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Why on earth do you want a PDF from an ebook? PDFs are to proof paper prints, or send to someone that will print on paper.
Export from Calibre as RTF or HTML, then use LibreOffice Writer OR MS Word, or a dedicated PDF creation program to create a PDF with the desired page size. You may want to edit styles or images to suit the PDF depend on page size.
A PDF is ALWAYS associated with a physical page size.
PDFs are not ebooks, they are electronic proofs for paper. Sometimes used as an envelope for multiple scanned images from a physical book or magazine when text isn't available, though multipage TIF is better if you are doing OCR.
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