See my complaint here: Reproducing the toolchain used by Xcode
I find it endlessly frustrating that Xcode ships with a Clang that is substantially different from anything in open source, even from Apple's llvm fork. There are clearly a number of problems with implicitly-generated modules in open-source Clang that are not present in the one that ships with Xcode; it would be lovely if Apple would publish those fixes if only to their own fork. There also seem to be a bevy of smaller changes, some of which are in the main branch in open source but not cherry-picked to the 5.5 release branch.