The final things that the install.linux.refresh.4.pl script does is to re-write configuration files on the build machine such as the network configuration, /etc/fstab, X-server config, inittab, etc.
That's all that's needed to rebuild a Linux machine. No reboots necessary. No scripted installation of applications, etc. I suppose you could have setup commands that would run after the machine reboots into Linux the first time but in a properly designed OS you really shouldn't HAVE to do that.