rpm has a hard-coded path to /usr/share/misc/magic for looking for the magic file, this should not be hard coded. Also a number of /usr/lib/rpm/binaries need wrappers in order to redirect where they get their macros from. This fix for this is to change the macro's file definitin of %_rpmfc_magic_path from /usr/share/misc/magic to %{_usrlibrpm}/../../share/misc/magic, and then ensure that the rpm-native binaries all have wrappers so that usrlibrpm is defined correctly. Thanks to Mark Hatle for helping with this.
http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=a5cf5ebd4a3d91667cd40e5d751b91facab16155