If you don't want the final text in the document to be bold and highlighted yellow, remove that formatting from the document before automating. You don't need these to draw attention to the document, since all of the placeholders will be in the turnsheet, meaning end-users can't miss anything. If you don't want internal bubble comments and footnotes in the final document, remove them from the document. Either put these internal notes directly in the placeholders or else build user interfaces that make the choice straightforward without the extra explanation.