A native PHP version is a version from the official repository of an operating system. It is installed automatically with ISPmanager. You can install alternative versions from the CloudLinux repository. To do so, go to Web-server settings → Install PHP and click on Install. PHP versions are installed in /opt/alt.
In Web-server settings → PHP you can see the versions available for every PHP mode. For more information please refer to the article PHP modes on CloudLinux.