This is an old post, but the real problem with the standalone compile you tried to do is that you used the wrong command, because you were mislead by Module::Build. When running ./Build, it prints out a command line it is using to compile the c files, but it prints it out incorrectly. When it runs the command, it bypassed the shell, which means that the quotes it shows are actually passed along to cc. As a shell command, it would be running the equivalent of:

cc -I/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE "-DXS_V
+ERSION=\"0.011\"" "-DVERSION=\"0.011\"" -c -arch x86_64 -arch i386 -g
+ -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protect
+or -Os -o lib/PerlIO/Layers.o lib/PerlIO/Layers.c
[download]

This means that the errors you saw in your standalone compile don't reflect whatever errors there were in a normal compile of the module. Any further diagnosis would require the output of a normal ./Build.