The aim is to let the author to focus on editing the site specific files under webapp/ and allow creating a Debian package containing the web server and an init.d script to manage it with dpkg-buildpackage.
The upside of using this option is that make-klone-project will be agnostic about the working directory, as long as it is somewhere inside the project tree, just like dpkg-buildpackage. The downside is that you run a greater risk of having the clean command cause unwanted data loss, if you happen to have an unfortunately named file in a wrong place.