But you can still see: is the source of this code something the user has written in a .c file, or something that came from a header file or from macro expansion, and only warn about the former. Granted this is difficult, because LLVM is multi-layered, but it's not impossible in the general case.

I think it's extremely difficult, to the point of not being practical. When you get to the point of the compiler that it's applying these optimizations, that the code came from a .c or .h file has been long thrown away.