The ability to specify at a finer level of granularity than directories sounds wildly overcomplicated, to be honest. I'm not aware of any other language that works at that level either (maybe Python's import mechanism does let you tinker at that level, but it would be extremely niche). Also, I'm also a bit confused about how it can work even in C/C++; surely most compilers don't even have the capability of specifying header file locations on an individual level, as opposed to the classic -I switch (or /I for Visual Studio).
I've used generated header files (protobuf) with CMake and they work fine. Although I prefer to create them at configure time rather than build time, even though that's philosophically incorrect, just because that way I can see them in the generated IDE projects and they don't break autocomplete.
I have used Buck for many projects, and in practice it is not complicated all... in fact I think it might be simpler. The reason why is that you define the includes relative to a single path, and the layout is just a Python (well, Skylark) dictionary in the build system. You never have issues with includes happening from the wrong paths, or the build breaking because files have moved around and someone wasn't including things in the correct way. Proper globs are also amazing from a build maintenance perspective.
I've used generated header files (protobuf) with CMake and they work fine. Although I prefer to create them at configure time rather than build time, even though that's philosophically incorrect, just because that way I can see them in the generated IDE projects and they don't break autocomplete.