The difference between selecting both options and deselecting them is:

When installing to /MITK/ the following directories are installed if the options are selected.

/MITK/include/ctk-0.1
which contains folders for all ctk style plugins of MITK, which in turn include the *_Exports.h

/MITK/lib/ctk-0.1
which contains a plugins directory with all .dlls and .libs for the same plugins

The components seem to be added by CTK, grepping for their respective names gives:

CMake/ctkMacroBuildApp.cmake: DESTINATION ${CTK_INSTALL_INCLUDE_DIR} COMPONENT Development
CMake/ctkMacroBuildLib.cmake: ARCHIVE DESTINATION ${CTK_INSTALL_LIB_DIR} COMPONENT Development)
CMake/ctkMacroBuildLib.cmake: DESTINATION ${CTK_INSTALL_INCLUDE_DIR} COMPONENT Development
CMake/ctkMacroBuildLibWrapper.cmake: ARCHIVE DESTINATION ${MY_INSTALL_LIB_DIR} COMPONENT Development)
CMake/ctkMacroBuildPlugin.cmake:# ARCHIVE DESTINATION ${CTK_INSTALL_LIB_DIR} COMPONENT Development)
CMake/ctkMacroBuildPlugin.cmake: # DESTINATION ${CTK_INSTALL_INCLUDE_DIR} COMPONENT Development
CMake/ctkMacroBuildQtPlugin.cmake: ARCHIVE DESTINATION ${CTK_INSTALL_QTPLUGIN_DIR}/${MY_PLUGIN_DIR} COMPONENT Development
CMake/ctkMacroBuildQtPlugin.cmake: # DESTINATION ${CTK_INSTALL_INCLUDE_DIR} COMPONENT Development
Libs/Testing/CMakeLists.txt: DESTINATION ${CTK_INSTALL_INCLUDE_DIR} COMPONENT Development
CMake/ctkMacroBuildApp.cmake: RUNTIME DESTINATION ${CTK_INSTALL_BIN_DIR} COMPONENT RuntimeApplications
CMake/ctkMacroBuildLib.cmake: RUNTIME DESTINATION ${CTK_INSTALL_LIB_DIR} COMPONENT RuntimeLibraries
CMake/ctkMacroBuildLib.cmake: LIBRARY DESTINATION ${CTK_INSTALL_LIB_DIR} COMPONENT RuntimeLibraries
CMake/ctkMacroBuildLibWrapper.cmake: RUNTIME DESTINATION ${MY_INSTALL_LIB_DIR} COMPONENT RuntimePlugins
CMake/ctkMacroBuildLibWrapper.cmake: LIBRARY DESTINATION ${MY_INSTALL_LIB_DIR} COMPONENT RuntimePlugins
CMake/ctkMacroBuildPlugin.cmake:# RUNTIME DESTINATION ${CTK_INSTALL_LIB_DIR} COMPONENT RuntimePlugins
CMake/ctkMacroBuildPlugin.cmake:# LIBRARY DESTINATION ${CTK_INSTALL_LIB_DIR} COMPONENT RuntimePlugins
CMake/ctkMacroBuildQtPlugin.cmake: RUNTIME DESTINATION ${CTK_INSTALL_QTPLUGIN_DIR}/${MY_PLUGIN_DIR} COMPONENT RuntimePlugins
CMake/ctkMacroBuildQtPlugin.cmake: LIBRARY DESTINATION ${CTK_INSTALL_QTPLUGIN_DIR}/${MY_PLUGIN_DIR} COMPONENT RuntimePlugins
CMake/ctkMacroCompilePythonScript.cmake: DESTINATION "${MY_INSTALL_DIR}" COMPONENT RuntimeLibraries

User zelzer has pushed new remote branch:

bug-16812-avoid-third-party-install-commands

This need a core change request because the CMake code in CppMicroServices was modified to skip install commands in case a special CMake variable was set.

[151e98]: Merge branch 'bug-16812-avoid-third-party-install-commands'

Merged commits:

2014-10-30 20:12:25 Sascha Zelzer [983796]
Do not trigger install commands from CTK or CppMicroServices.

2014-10-30 20:10:25 Sascha Zelzer [668db0]
Merge commit '830daf03dbe6783f425d6978c7de724fd87ff6fb' into bug-16812-avoid-third-party-install-commands

2014-10-30 20:10:25 Sascha Zelzer [830daf]
Squashed 'Core/CppMicroServices/' changes from 7527117..0ebe6b8

0ebe6b8 Do not install artifacts if US_NO_INSTALL is set.

git-subtree-dir: Core/CppMicroServices
git-subtree-split: 0ebe6b8c1f99e3e5baab063212d0753e99ef087d