You'll probably want to start this thread in the Designer forum. Our current understanding is that they will allow both - having Designer effectively import the metadata for resolving/modeling purporse, but not include it in the VDB, and importing the metadata for inclusion as source models.
In Komodo, we're utilizing the Teiid API to expose source metadata as "proxy"-type objects. The default behavior will be to NOT include the source metadata in your VDBs and assume the metadata is loaded by Teiid runtime by just defining the <source> properties in the VDB manifest.
As we move forward, we'd be interested in your take on what your web-based tooling. We've working on both an Eclipse prototype and a Web UI editor.
Teiid Designer Project