The custom polly-check-format target runs clang-format over all source files in the directory tree excluding lib/External. isl_config.h is a header file that is generated by CMake in the build directory, and it's not correctly formatted (which I also wouldn't consider necessary, as it is a generated file).
If the build directory is actually inside the Polly source directory (which it might be if you're building Polly out-of-tree), that check always fails. Hence this patch excludes this file from the check-format target.