@greatninja3
1) From what I understand, a male-to-female emergence at 17 years old is rare. Most emergence happens during childhood. It was mentioned in the early chapters. That's why a lot of pple were shocked when Mamiya emerge during high school.
"...for cavemen to have a male in the group to turn into female and they maybe have an orgy with that female (just like a clownfish)" --> this sentence gave me the impression that you were thinking of e.g. 5 men sitting around in a cave, the last of their tribe coz some disasters killed off all the people who were born females, then poof! One of the men became a woman after 'emerging' from a cocoon, then the men have orgy with the woman. But emergence is supposed to happen during childhood. I'm not even sure there would be polyandry.
Throughout human history, polyandry is not common because it doesn't make as much biological sense as polygamy. In polygamy, the man can put the buns in as many ovens as possible simultaneously, but in polyandry, no matter how many husbands, there is only one oven. Societies that practiced polyandry were either (a) matriarchal, so the husbands (through 'walking marriage') aren't recognised as fathers, and the kids were raised by the brothers of the kids' mom, or (b) Fraternal polyandry, in which a woman is married to two or more men who are brothers, mainly for the purpose of not splitting family land to unsustainable small plots.
May be the strongest man ended up marrying/staking claim to/impregnating the "emerged" woman, and any genetic superiority was half (or almost entirely) attributed to that strongest man.
Sure, 'emerged' women might have been treated well during tribal era due to necessity, but to be treated as divine beings... I don't think so.
2) As you said, "it’s just recently humans are able to map human genome". So most probably don't realise that some of the babies of "emerged" women weren't fathered by any men. Rats have really short lifespan but humans develop over long periods of time and prove their superiority through different ways (e.g. book smarts vs better muscles vs better intuition). During tribal era, infant mortality was incredibly high, so it's possible a lot of intelligent babies born from "emerged" woman died before other people noticed they have bigger brains.
So by the time people are able to observe that descendants of "emerged" women are genetically superior indeed, may be it was only during renaissance and the whole 'envy against genetically superior people' culture already developed, making the intellectual descendants hide their identities.