When you start an AS7 (I used EAP 6.0.1) server and then change deployment to workspace metadata and save it on the fly, you will notice that the server gets synchronized, so I would assume that the change is applied (and new deployment scanner is created), but when you then deploy something, it isn't deployed.

After restart the new deployment scanner is added to the server.

A side issue: Of course the .dodeploy marker stays in the deploy location, because the server doesn't pick it up (the deployment scanner is not set up), but when I delete the module from the server, at least then the .dodeploy should be removed if it's still there - currently it stays there.