Hello,
The problem comes from the first template and how Word works with headers and footers. By default Word adds headers and footers in all pages and you need to set where you want to add or not them. You can change headers and footers adding new sections.
To solve this issue you have two approachs:
1. Do an intermediate merge to add a new DOCX with the new section that doesn't include any header nor footer.
2. Add in your first template a new section that doesn't include the header and use the mergeType as 1.
This page explains how to delete a header or footer from a single page:
Regards.