Remove header and footer is supported by all formats. What happens is: the input (no matter what format) is converted to html and run though a preprocessor before being turned into an internal OEB book. The preprocessor applies the regex to remove the header and footer as well as doing other things. The OEB is then turned into what ever your output format is.
PM me your PDF and I'll look at it to see what kind of regex you will need to remove the header and footer.
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