The problem is the half of the teams that pass through are 24. To fix the disparity they select the 8 best relegated teams and let them through.
They added a 32 team extension to the knockout stages to make the tournament last an extra week and increase audience retention.
It is not clear why they didn't want 16 groups and settled for just 12. I would speculate that the group stages would last too long and the least skilled portion of the league would be too much worse than the best teams causing embarrassment to the nations, they would get scores like 16 - 1 or something like that.