Ugh, ok, I got it to compile as a universal binaries but the plugins and libraries got mutated. libtool obviously has no idea what to do :-/. Having universal binaries is going to be a lot of work unless either Code::Blocks add universal binary support, or C::B switchs build systems.
EDIT: Well, I got a universal binary, but plugins are completely broken - it only loads if I move it out of the way. It appears the problem is the plugins are built as bundles instead of libraries, which are not universally supported, hence why it blows it. The build system going to require major work to make this work well.