The Windows setup program should not be used for production deployments.
It is meant for evaluation purposes so users don't have to install and configure an application server and database before they can see Clearspace. That is why the setup program installs an embedded application server (Jetty) and an evaluation database.
Not only is there no advantage to using the Windows setup program in terms of upgrading. It would actually make upgrading more difficult.
Hopefully the README document provides clarification: http://www.jivesoftware.com/builds/docs/clearspace/latest/README.html