You can now edit an existing build configuration. Click on the menu icon called More Actions... on the build directory in the Applications panel, and then click on Edit Build Configuration. This opens a new tab with a form for editing the build configuration parameters. Once you are finished, press Generate Configuration to regenerate the build configuration and overwrite the contents of the build directory.
The Extra CMake Arguments field is populated by inspecting the CMakeCache file. It is only possible to populate CMake variables declared with the -D command line option and not other command line flags, as there is no record of them being stored in the build.