OK, I see the problem. Do you think it would help if it tested both
sys.executable and its symlynk-resolved path against sys.exec_prefix
like this:

            if sys.executable.startswith(os.path.join(sys.exec_prefix, "bin")) or
                os.path.realpath(sys.executable).startswith(os.path.join(sys.exec_prefix, "bin")):
                # building third party extensions
                self.library_dirs.append(sysconfig.get_config_var('LIBDIR'))
            else:
                # building python standard extensions
                self.library_dirs.append('.')

Alternatively one can reverse the test. I guess that 'else:' is supposed
to apply when one builds new Python installation? Where does the 
sys.executable points to in this case? Is there any other (more reliable)
way to figure out that the standard extensions are being built instead of
third-party modules?

Andy