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Hi,
Mainteanance will overwrite any other plugins or code from loading on the Maintenance page to prevent errors and unintended content to be displayed while you are working on the website.
So you will have to change it in the template file. If you are comfortable editing code you can add your header in load/index.php around line 40
In the PRO version we have the option to return a 503 (unavailable) status code to prevent search engines from indexing the page.