You are not trying to install a subdomain multisite into a subdirectory.
You are trying to install subdomain multisite into a subdirectory which is not supported by WordPress.
Installing a subdomain multisite into a subdirectory (e.g. http://example.com/subdirectory) is not supported by WordPress.
If you still want to install the multisite in a subdirectory proceed with the installation as usual and after finishing it manually edit the wp-config.php and database to turn your subdomain installation into a subdirectory installation.