That makes some sense.
It did seem weird.
I have an answer for you. It's not very interesting.
In the round of 16, The winners of groups A,B,C&D get to play "best 3rd place teams". But (and this is important) the winners of groups E&F get to play runners up (not 3rd-placers).
Now each time they arrange a fixture of group winners v 3rd placers, they avoid choosing the 3rd place team from the winners group. With me so far?
Now if the 3rd place team comes from E or F this clash never happens because their group winners are playing runners up.
So each time they arrange one of these fixtures they choose the 3rd placer from E,F or one other of ABC or D that is in the opposite side of the draw.
So winner A's opponent is chosen from E, F or C because C is on the opposite side.
The end result is that E and F occur more often in the possible picks.
If that didn't make sense, don't worry. You're not missing much.