The site config files in the SDK are incorrect. They are missing the glibc configurations -- or in some case (multilib) may even end up with incorrect settings. The meta-environment calling the toolchain-scripts functions does not properly look for the right site-config files, instead it references the nativesdk host's files.
OE-Core Commit: 1f05aaa4944ddac6c2b3ba440effdf1eaf732656