Package Installer from CB Package Builder uses Joomla installer API to install extensions. There is nothing wrong with doing it this way. Admin Tools is not Joomla core. Whatever protections it applies has nothing to do with what is and is not allowed. We're using perfectly valid and safe API. Package Installer completely removes itself once completed as well. Package Installer allows us to generate custom installers including any number of our components, modules, plugins, and cb plugins.
It's also done this way because Joomla extension installation is terrible for large packages. A standard Joomla package would install everything at once without a chance to clear memory. Package Installer installs extensions 1 by 1 using ajax calls to clear memory. This means a large package with even 100 extensions cannot crash your site.