Thanks for clarifying. There’s likely a server misconfiguration that affects the signature URL if the signature isn’t showing up on the Entries page. When using the Signature field merge tag, a URL to the signature is returned. This is why your custom template isn’t working.
For speed, Core PDF templates use the absolute path to the image instead of the URL. That is why the signature works in those PDFs.
To fix your issue, you’ll want to swap from merge tags to the $form_data array for outputting the signature: https://docs.gravitypdf.com/v6/developers/php-form-data-array#signature
If you have any other issues, please open a new support ticket.