The stating of the question implies an agenda but I'll do some answering anyway.
For one, I was disappointed to see no mention of Vera Menchik here. First women's world champion, she defeated many of the best males of her time, including World Champion Max Euwe (twice!) as well as Sammy Reshevsky, Jacques Mieses, and Lajos Steiner. Hastings 1930-1, Euwe lost only one game in the entire event -- to Menchik.
Now, the OP states, without any visible support, that the disparity of cannot be explained by population, but that's something my own experience of over a decade organizing a good portion of the strongest events in my state leads me to believe is absolutely true. The percentage of female chessplayers in the events I organized was well under 1 percent of the total players (in close to half of those events, it was 0). And if, over that same period of time, we decide to use total unique players (every individual counts as 1 player, no matter how many events of mine they played in) that number would be no higher. Hence the disparity in number of players would easily explain the population difference in the top 100. In fact, I'm impressed there are 2%.
Moving on from that, I've yet to see anything prove the popular notion that chessplayers are smarter than the general population. We can all think of top-level chessplayers who have advocated some pretty hare-brained ideas. I've known a number of very smart people who never proceeded past beginner levels in chess, and others who did. Weak correlation at best, it seems to me.
I think we should dismiss the "genius" allegation in the original question the same way. No proof for it at all.
One of the more interesting fields for this study is in the very young players. In the USCF lists the concentration of females in the top 20 or top 100 lists is higher at the earlier ages than later, with numbers at 10% or more being female on the young lists, going down to 2% or so on the older ones. This parallels my experience as a chess coach; there were more female students in my younger classes than my older ones.
I've spoken to some of the more promising ones about why they stopped. Reasons for walking away from chess were varied. Some did it because of what we would term "socialization" -- they felt pressure from the outside world (peers, family members, other authority figures) to stop playing chess because it just wasn't "something girls were supposed to do." Some did it for the same reason males walked away later in life -- they got too busy, or became more interested in other things (from social pursuits to STEM subjects such as Chemistry or Math).
But for some, the reason was the boys. Not more interested in boys than chess, but less interested in chess because of the attitude of the boys playing it. I know several girls who continued to read about chess, just never showed up or sat down to play it at a club because of the tendency of the boys of similar age (pre-teen to teen) to denigrate them. (The denigration, I can attest from observation, came independently of skill, in fact, the better the boy was at chess, the less he tended to sneer at the girls who played well. It seemed more an outside-the-game tactic employed to keep mediocre boys from losing to a better player. Viewed as such, I would have to say it worked; if she didn't play, it was one less threat for him to face.)