Re: Is there a cleaner approach which would simply allow me to have the changes flowing into my r&d repository workspace without the need to constantly add the main stream flow target?
To simplify your manual syncing of streams, you don't need to explicitly add/remove the main stream to your r&d repository workspace list of flow targets. In the Pending Changes view, if you are showing your r&d repository workspace, you can select "Change Flow Target..." from the context menu and easily switch between main and r&d. This will add the stream to the list of flow targets and set it as current. The default flow target is really only important for a build workspace.
I noticed you also created a repository workspace off the main stream, but don't mention it in your process. It is really unnecessary, as you're only using one repository workspace.
Scott