During the upgrade process, the iManager 2.5 installer removes the Tomcat4 directory if it cannot detect that Tomcat is already installed. The 2.0.2 installer installs enough Apache files for the 2.5 installer to determine that Apache is installed, so that it does not try to reinstall Tomcat.
The upgrade is seamless in that the Tomcat setup from 2.0.2b remains the same: Tomcat functions as both Web server and servlet container. The installation displays Apache as being installed on the detection summary screen, when, in fact, it is not. Simply ignore this and continue through installation.