Doesn't this just allow an end-run around the license by allowing you to distribute a program that embeds LLVM, whose only purpose is to be an LLVM wrapper to avoid those sections of the license?
That is intended to mean that if the compiler copies in some binary code (to implement a compiler primitive or the like), that it doing so does not require you to treat that code like it is licensed under the LLVM terms.
Note that the LLVM source code is not "your source code", so simply copying in the LLVM source and compiling it will not trigger this exception.
That is not to say that there might not be a loophole. E.G., modifying LLVM to always copy all of its binary code into the resulting exececutable (and licensing those changes under this license), and then compiling a program that wants to embed LLVM. I'd like to think that courts would refuse to allow such abuse, but who really knows.