You must not include /root/ispconfig/scripts/lib/config.lib.php in your install.php because then ti will not run with root privileges.
/root/ispconfig/scripts/lib/config.lib.php is called by /root/ispconfig/writeconf.php which itself is called by the /root/ispconfig/sv/ispconfig_wconf daemon which runs as root. This /root/ispconfig/sv/ispconfig_wconf daemon checks every 10 seconds if a file /home/admispconfig/ispconfig/.run exists; if it does, it calls the writeconf.php script.
So you have to modify /root/ispconfig/scripts/lib/config.lib.php and/or /root/ispconfig/scripts/writeconf.php, and whenever your install script is called, it should create /home/admispconfig/ispconfig/.run (add
to your PHP code) so that writeconf.php is called.