I asked the CIF basketball person about this, and I think she willfully misunderstood.
Let's say there are 1000 schools in the South (they don't have that many) and 500 in the North.
If all things were equal and you ranked the schools from 1 to 1,500, assuming each region was equal in ability, you get this percentile ranking for Division 3 if each region had the 25th through 40th best teams:
The North's 25th through 40th teams would range from the 92nd percentile to the 95.5th percentile.
The South's 25th through 40th teams would range from the 96th percentile to the 97.5th percentile.
Now in reality the two would be intermingled, meaning the teams in question would be 25th through 64th, but that's too much math for me, so I went with the easy route that makes the same point.
It gets worse the further you go down, and though of course there's far from a guarantee that the team in the 97.5 percentile will beat the 95.5 percentile, the fact that the South's worst team in Division III would have a higher percentile ranking than the North's best is an issue.
I don't foresee a running clock, because any team that reaches a state final is a good team, but the days of the North salvaging respectability by winning lots of small school state titles are going to be over sooner rather than later.