Pathagoras can process <<*Options* . . .>> and <<*Optional*. . . >> text blocks in your header and footer, with one caveat. Make sure the options/optional block in the header or footer is tied to a 'parent' block in the body of the document via a !groupname!
Caveat: 'Free-floating' Options and Optional text blocks (with their own set of prompts) will not be processed. (If you do not otherwise have a !groupname! link, just use an <<*AskOptions*!group!. . .>> or <<*AskOptional*!group! . . .>>