I should have specified that the failures I saw were just with the default intel-64 arch on the beta.

After thinking about it a bit and reviewing the code, I think the best approach is to handle this in _osx_support.py as part of the compiler flags customization.  What's been happening over the years is that Apple has been deprecating and then removing system header files and system library files on running systems and instead forcing the use of an SDK to build with for both. That's fine but, to continue to support a range of systems, we should be able to handle the various default configurations when the user does not explicitly specify a particular SDK to use. The Apple compiler chain does the right thing under the covers so that C compilations just work. setip.py's macosx_sdk_root() now has initialization code to discover the path to the system header files that the compiler is using; it calls the compiler with -v on a dummy program and then scans the compiler output for the include paths searched until it finds either /usr/include or a path ending in .sdk/usr/include. (It's a bit of a hack but a fairly widely-used hack that works with both clang and gcc, at least, and for the Apple-supplied compilers, takes into account the dynamic specification of SDK via xcrun.)

I think the thing to do is move that sdk path detection into _osx_support and then, at the end of other customization steps, if there isn't already a valid -isysroot provided by the user (either through ./configure or CFLAGS et al, add a -isysroot for the discovered default SDK path (or /) into the appropriate customized compiler and linker flags. It would also provide a function to return the SDK path for setup.py (the equivalent of the current macosx_sdk_root()) and others to use. setup.py and Distutils should then do the right things for both header and library file paths on any configuration (whether header files are installed or not and whether lib files are installed or not, Command Line Tools or Xcode) and, with luck, any other Distutils replacements that also use _osx_support will also do the right thing.

I had contemplated removing _osx_support at some point in the future but, now with the return of universal files, I'm glad we didn't.