Checking this option did not prevent the background shape from creating, because the original EPUB file doesn't have any background to be removed. It's something that the converter ads on its own in every exported PDF.
I've downloaded fresh Calibre on my Windows PC and the same thing happens with the demo EPUB that came with it. You can test it, just export any EPUB file to PDF and then edit that PDF somewhere (I'm using Adobe Acrobat) and you'll see the rectangular white shape on each page.
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