this is install section. RPM in %files section recognize list of packages and directories that is owned by this rpm and if it is uninstalled it is uninstall as usually. So this part is used only to install to RPM_ROOT and only things that are marked in %files section is taken to rpm metadata. So uninstall work as expected. BTW it is recommended workflow for manual installation in rpm documentation - http://fedoraproject.org/wiki/How_to_create_an_RPM_package#.25install_section