Starting with GCC 8, GCC has added support for prefix remapping of the __FILE__ and __BASE_FILE__ macro similar to the handling of -fdebug-prefix-map. It also adds support for -ffile-prefix-map, which is simply the union of -fdebug-prefix-map and -fmacro-prefix-map.
A not unreasonable alternative is to have -fdebug-prefix-map also apply to the macros. That seems to be the approach taken by the Yocto project in its local patches to GCC.
I created a review for this. https://reviews.llvm.org/D49466
This has finally landed, thanks Dan! https://reviews.llvm.org/rG6c92cdff72251a7d13ab3958b04fba72dfcaebb1 If everything goes well, this should become a part of Clang 10. @Dan would you mind writing a release note entry?