There are a number of possible reasons.
Until very recently, L3s in the South would referee step 3 and 4 football, whereas in much of the North L3s would be refereeing at step 5. There is an argument to say that officiating higher level games makes it trickier to get promotion as it is a national merit table.
In the South, especially around the London area, refereeing at senior levels can be that much harder as they often work in London and use public transport, so they have to leave work to go home and get the car before travelling to the game. I know of lots of senior referees, myself included, who cited that as a reason they didn't carry on as it was just too difficult to balance work and refereeing.
And the final possible reason might be the transient nature of people in the South East. A lot of people start refereeing down here when they are young but then move away as they are older and start families. I can think of at least three current EFL referees that were trained and came through the system in London and surrounding counties, but now have moved away.