Because of the way that partial signatures work, only the last party to add to an exchange can add metadata in a separate output.
However with MultiChain 2.0 (alphas) you can add inline metadata, which is metadata that sits inside a regular transaction output. This will go into the output added by whoever calls appendrawexchange. Example:
appendrawexchange [tx-hex] [txid] [vout] '{"asset1":100,"data":{"json":[1,2,3]}}'