It is not only finding X11/Intrinsic.h that fails. It is only the first
header in line after _BSD_SOURCE and _SVID_SOURCE has been added to
confdefs.h. So the problem lies in the general way header files are
detected.

A workaround is then to silence cpp when it comes to #warnings. This can
be achieved by running configure with --cpp-flags=-Wno-cpp.