My first thought is that additional warnings from Duck, whether manually or automatically given, may not have been seen or heard by a tug mate who already hadn't heard radio calls on ch. 16, nor seen what should've been a good contact on his radar. There are limits on what a small boat can do to correct an unseeing unhearing watchstander or lookout on a larger vessel.
One thing that might have helped is the tug putting a range warning alarm, or 'guard ring' on his radar, so that any contact getting close would've triggered an audio and visual alarm.
Thinking into the future, how about a warning alarm on the larger vessel that can be activated by a signal from the smaller one? Used to be this way on the old morse code sets, an SOS from one ship would trigger a loud alarm in the radioman's office and stateroom on another. Maybe they could rig up something like this on a local basis, that would trigger a larger vessel's GMDSS or AIS system.
which brings up the other question--did tug have AIS, and did Duck have at least an AIS transponder?