Canvas Credentials can be installed at the account or sub-account level, but the only option is to have it display as enabled by default in the Course Navigation Menu. According to Support, there used to be an "XML install option for the legacy LTI that allowed you to have the Badges menu item disabled in course navigation by default, but this feature has not been built into the newer 1.3 LTI."
Please consider building this feature into the newer 1.3 LTI so that Credentials can be installed at the account and sub-account levels as disabled by default in the Course Navigation Menu.
