I believe that the PDF output option of Calibre does not support top and bottom margins.
As far as I know there is little interest from Calibre developers in enhancing PDF output so this is unlikely to get resolved any time soon. PDF is seen as an undesireable format for ebook devices, and is supported primarily for legacy reasons. Calibre's prime focus is on the main ebook formats such as epub and mobi, and on adding capabilities that apply to all formats.
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