There is a good reason why there is this line in the setup script. About 300 - 500 users install ISPConfig every day and you are the first one that had to remove this line.
If you install ISPConfig and run the setup script more then once because e.g. the installation stopped due to a dependency missing during compilation, then the install_ispconfig folder has to be removed.
I guess you accidently tried to install ISPConfig from a folder /root/ispconfig or similar, which is used when ISPConfig is isnstalled.