VaultWiki looks for a setting called 'copyrighttext' (which doesn't exist in XenForo). If it exists, it adds its copyright text to the end of it. This is the vBulletin behavior. I can only see this causing a problem for XenForo if a different mod creates a setting called 'copyrighttext' (since XenForo doesn't have one) and still adds their copyright to it even though their branding removal is applied.
If you purchase VaultWiki's branding removal option, that's how it works. The copyright string never gets created/appended. It has nothing to do with templates or template mods.
'copyrighttext' is generically named so VaultWiki expects it to be the site value if it exists. All of VaultWiki's own settings use unique identifiers, so that is a moot point. As I posted above, you can override this by making VaultWiki look for a copyright string with a different name with the code I posted.
Ideally though, it would match your existing copyright string if one exists. That way all your copyrights appear in the same place even if you modify your footer template. That is why I said there is something wrong with the way branding removal is handled by the other mod.