The Territory hard border with NSW has nothing whatsoever to do with being able to
transit through Darwin airport.
In the same manner as if you flew from Hobart-Sydney, overnighted in Sydney and then caught your flight to Darwin,
you are not taken to have been in a Covid hotspot. You are not "entering the NT" until you leave Darwin airport per se' - and the NT allows travellers from
outside a hotspot to transit
through a hotspot to get to the NT if needed, by staying overnight. Same as I currently hold valid passes to enter both Qld and Victoria so long as I do not leave the airport grounds and then fly back out of the state - but I cannot enter either by road.