Of course, we all know what Kyubey's implications are worth. Maybe we would have been living in caves without Incubator intervention in his opinion not because he has actually been around before human civilization came into being, but because he showed up during the Cold War and one of the first wishes was that there wouldn't be a nuclear war. He assumes, because he considers us all insane anyway, that we absolutely would have bombed ourselves back to the Stone Age and used that to imply his presence on Earth much earlier than he actually had when trying to manipulate Madoka.
I think I like that one a lot, since it would imply he was aping pre-existing Magical Girl media for his system in order to make everyone easier to manipulate rather than Magical Girl media coming about as Kyubey deciding to help produce propaganda. And in general it makes the butterfly effect less problematic between our real world timeline, the Witch timeline and the Wraith timeline the shorter the period of history Kyubey's been messing with.
Sure, this doesn't work with Tart, and makes the historical Magical Girls trickier, but multiverse theory could put those girls in alternate timelines where Kyubey showed up at different points in time.
The issue with that theory is that in that conversation where Kyubey makes the "you'd probably still be living in caves" comment, he does also pretty explicitly say "We have been involved with your civilization since before your recorded history".
Plus, he showed a bunch of images of historical magical girls in that conversation too, and I don't think that he just made those up or that they were from alternate timelines or something.
...But yeah, that does leave us with canon being pretty weird in regards to magical girl media and the butterfly effect.
If we're going to ask Kyubey things just to satisfy our curiosity, I still want to know where he got the idea boys aren't as emotional as girls. I could see him just not understanding emotions and uncritically accepting pop culture stereotypes, but if he's been around as long as he implies he has, the pop culture stereotypes about that would have reversed more than once during his time here.
I am kind of curious about this too, though. Kyubey's wording in the translation I watched is:
Kyubey in episode 9 said:
"Your souls are energy sources capable of defying entropy. And the most effective of all are girls in their second stage of development, who experience the greatest fluctuations between hope and despair."
Which, to be fair, "experience the greatest fluctuations between hope and despair" isn't
exactly the same as saying "girls are more emotional"... But even then, the idea that girls undergoing puberty just universally experience greater fluctuations between hope and despair than boys and adults to such a degree that it's not worth performing the process on anyone else is still kind of absurd.
This probably isn't the intended way to read that line, but one
could read the "who experience the greatest fluctuations between hope and despair" part as not intending to explain why teenaged girls are most effective, but rather as further specifying what kind of teenaged girl is most effective. Aka, "And the most effective of all are those who
both 1: are girls in their second stage of development, and 2: experience the greatest fluctuations between hope and despair."
In that reading, Kyubey considering teenaged girls most effective could be for a completely different reason than "girl experience the greatest fluctations between hope and despair". Like, their tech just being generally best adapted to working with teenaged girls or something, in which case that says more about the limitations of their technology than about the nature of teenaged girls.
As one example, maybe they need to do some medical trickery to both rip the soul out of a body and keep the body functioning with its soul ripped out, but whatever trick they use doesn't work as well on bodies that diverge too much from particular hormone balances or sets of sex characteristics or something. In which case whether it would work on intersex people would fluctuate wildly, it would
probably work on someone AFAB if they're not taking hormones, it would
maybe work on someone taking estrogen, and would probably
not work on someone AMAB and not on HRT, though it might if they wish for bodily changes or something?
(Ultimately, though, when it comes to the "why does kyubey only do magical
girls" question, I tend to mostly just go "eh, genre conventions" and just try not to think about it too hard)