Hello,
Yes, setting the mergeType option as 0 in the mergeDocx method keeps the section (including headers and footers). You need to use the MultiMerge class to accomplish this task; this class is only available in Advanced (old Corporate) and Premium (old Enterprise) licenses, but not in the Basic license (old Pro).
As your username doesn't have a tied license, please send to contact[at]phpdocx.com the username or email of the user that purchased the license, the DOCX before merging them and the merged output.
Regards.