Please correct me if I'm wrong... but neither Docky nor Gnome-Do have been accepted as official gnome components or even as external dependencies under the definition of the Gnome desktop as defined by the Gnome Project.
To my understanding neither gnome-do nor docky have been proposed for inclusion into the GNOME desktop in this round of module proposals even though I've seen some sidebar discussion around such a proposal. gnome-do which docky depends on overlaps with gnome-shell, so again, just like with libappindicate its not clear how docky/gnome-do integrate with the Gnome 3.0 roadmap.
What I see happening is that Canonical is intent on creating a differentiated desktop environment that is distinct from what the GNOME upstream project is doing. And that's fine and dandy... but how much differentiation can they do and still claim its a GNOME desktop? Its one thing to add optional components that extend the GNOME desktop. Its quite another to deliberately remove components that are part of the GNOME platform and tell application writers they cannot rely on that standard GNOME functionality to be present. And that's what they are doing with the notification tray removal.