BundleUtilities: Fix treatment of .dylib inside .framework folders

The specific cause is when e.g.

    /Library/Frameworks/GStreamer.framework/Versions/1.0/lib/libgio-2.0.0.dylib

is detected by fixup_bundle.  set_bundle_key_values() interprets this as
a framework, thus doing a string replace that creates an embedded_item
that is equal to the original path, i.e. it is not embedded.