The Package originator can control how to protect the finalized executed documents and the downloaded MasterFile PDF by enabling/disabling certain security settings.
While creating and customizing a Package, click on the Security tab in the Package Options menu. Under the Security tab, there is a Protect toggle switch that controls the security settings/restrictions. When the Protect toggle switch is turned ON, the Package originator has the ability to activate/deactivate subsequent toggle switches for enabling/disabling certain security features as described in the screenshot below.
If you need to merge or manipulate the document in any way after a signing, you will need to disable the Protect option.