I have found that the PDF output obeys custom css rules specified by the oxf.fr.css.custom.uri.*.* property (the rules need to be targetted to print media with @media print, of course).
https://github.com/orbeon/orbeon-forms/wiki/Form-Runner-~-Configuration-properties#adding-your-own-css-files-orbeon-forms-4
I'm sure you could remove both header and footer with "display: none;"
Aaron Spike
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