Perhaps we should be asking why we have "two identical systems"?
Surely one would be designed for the known, predictable and repetitive movements of civil aircraft carrying the nations commerce - the other for the dynamic and unpredictable movement of military operations practicing warfare.
The latter is practiced not by ground based air traffic controllers but by air defence radar operators. These people vector aircraft to hit each other , not to keep them apart.
It follows then that when military aircraft are not practicing war-fighting they can be kept apart from each other by civil controllers. This would typically mean that all the nations airspace was available for the efficient movement of commerce and military aircraft simply moving through the airspace. This might mean from base to base or from base to the war-fighting area and then back.
When the military aircraft arrive in the war-fighting area whatever piece of airspace was required could be given to the air defence radar operators, civil traffic kept clear, and an hour later (what is the endurance of a hawk or F18?) the aircraft would again transit under civilian control and the exercise airspace return to commercial use.
I think that the Air Marshal is referring to the vast areas of Australian airspace that are excised from civilian use and controlled by RAAF ATC, they are Restricted areas, some the R3's which they never give civilian aircraft clearance to transit. This is where the identical ATC systems exist and where Australia differs from our other western liberal democracies.
Is it necessary and do we have to design a combined ATC system? I think not, a combined system could just as easily be civilian with the ADF getting whatever exercise areas they need on a daily basis and then handing the airspace back to the people.