If Auckland were to move to level 3 on September 14 as planned and to move to level 2 only a week later (rather than two weeks later), the first possible weekend of fixtures would be October 2 (as NZF wants there to be at least a week to prepare) and there would be 12 weekends between then and the weekend before Christmas.
Three weekends are needed to complete the Northern League (plus one midweek). 10 weekends are needed to complete the men's National League Championship. So a total of 13 weekends.
That discrepancy could be solved by making the National League Championship a round-robin with no final; by holding a double round of the National League Championship over Labour Weekend; or by adding an extra midweek round to either the Northern League or the National League Championship.
The document NZF distributed to clubs only outlines two scenarios – one where regional leagues begin September 25 (which won't be happening in the case of the Northern League) and the National League Championship begins October 16 and one where regional leagues are scrapped and the National League Championship begins October 16.
Obviously things are very fluid and Auckland spending two weeks at level 3 (IMO the most likely scenario, unless we get to zero cases per day fast) will mean no Northern League matches are possible until October 9. It would still be possible at that point to complete the Northern League and hold a modified National League Championship (say, two pools of five teams plus a final, over six weekends) but it seems the preference of NZ Football would be to find four Northern League qualifiers and get a full National League Championship in.