make sure to not warn about unused macros from -D

If a PCH is used for compilation, SourceManager::isInMainFile()
returns true even for the "<built-in>" predefines area. Using -D
only for the TU compilation may trigger -Wunused-macros for it.
It is admitedly a bit fishy to set a macro only for a TU and not
for the PCH, but this works fine if the PCH does not use the macro
(I couldn't find a statement on this for Clang, but GCC explicitly
allows this in the docs).

Differential Revision: https://reviews.llvm.org/D73846