config.test_extra_flags is passed in from lit.site.cfg.in files, but they're not used in the LIT configs. This variable can be useful for distros which don't have the standard c/c++ headers in the default search paths. Since the tests run clang on c/c++ source code, we rely on test_extra_flags to pass in the necessary header files.
This is a similar setup that's also done in litomptarget https://github.com/llvm/llvm-project/blob/master/openmp/libomptarget/test/lit.cfg#L42 and openmp/runtime.