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The Indigenous populations of the Americans came primarily from Asian populations around 18K years ago who underwent one hell of a trek. Funnily enough, 2 day old Navajo and Japanese babies show similar responses on the cloth over nose cognitive test (near complete docility) which would be extremely abnormal in caucasians. The separation between Africans and every other group is over 50K years. Given the standard theory that we all came out of Africa, it makes intuitive sense for the least cognitively capable members of our species to be the ones that didn't make it elsewhere. The Saharan desert is not exactly tolerant of the unintelligent.
Evidence for the horribly run nature of African societies, or malnutritution and parasite load doesn't exactly counter the validity of the genetic hypothesis. All of these are highly indiscriminate, killing the smart at similar rates to the stupid. You need particular conditions for selection pressures to favour intelligence over the simpler traits they might favour (speed, muscle, and high testosterone for example). Note that these are all areas where Africans excel, with African infants showing greater muscle control at birth than caucasians or asians (but not aboriginals).
I think the second half of your first paragraph has a bunch of issues.
I don't think it logically follows that the smartest would be the ones to leave first, especially in the context of simple, pre-agrarian hunter-gatherer societies. It could very easily be that the ones who left first were the least aggressive, and thus least likely to defend their territory. Inuit folklore mention the Dorset and state that their response to outsiders was simply to flee. I don't see why that wouldn't have been the case during the first human migration from Africa. I'd judge the argument that leaving Africa in the first place is a sign of intelligence to be false. Indeed, I think the low aggression hypothesis is actually more likely, given that there are experts who argue that drought in Africa is what first spurred the out-of-Africa migrations. That's a point in favour of aggressiveness/docility being the distinction between stayers and leavers, as conflict over increasingly scarce resources would have been inevitable.
Also, the first migrations out of Africa were fundamentally different than any that came after, as the original out of Africa population was traveling through areas where there were no Sapiens Sapiens, only Denisovans and Neanderthal. Once the first group leaves and is in the way, it becomes significantly less simple to push them out and then migrate, as you have to go through potentially(probably) hostile societies to do so. The first group to leave was incredibly lucky, and if they had been the second group due to minor changes in inter-tribe politics or random chance, they might never have made it out.
Finally, some parts of Africa are close to the Middle East and some are not. Any group that ended up in Southern Africa simply wasn't going to leave, and that is entirely circumstance and has nothing to do with any of their group characteristics. There's no reason the smartest humans 70,000 years ago couldn't have been denied the opportunity to colonize the world due to their location.
The Sahara was unlikely to have been a barrier to the first humans leaving, either. It has cyclical wet/dry periods, and it seems that a wet period ended ~70,000 years ago, which is right in line with the out-of-Africa migration that led humans into Eurasia and beyond. I find it more intuitive, given this fact, to suggest that the drought and desertification of the Sahara region was the impetus, and that it only became a hurdle for migration after the humans had already left Africa. On top of that, the Sans of Southern Africa have been successfully living in the Kalahari desert for 20,000+ years, despite scoring even lower on IQ tests(55 on average!) than other African groups.
With all that in mind, I find it very unlikely(I'd posit 95% confidence that this is the case) that the intellectual differences between Sub-Saharan Africans and non-African populations are the result of genetic differences that existed before humans migrated out of Africa. Any such differences are probably the result of selection pressures after the fact.
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That hypothesis, to be clear, was that high malnutrition rates and poor general sanitation leading to high parasite load take IQ points off of Africans. It's a competing explanation for African underperformance relative to other parts of the world which also produce few nobel prize winners. The explanation isn't evidence against competing hypotheses; I don't think that South Sudan with the social conditions of Holland or Japan would have an IQ of 100, I think it would have an IQ similar to blacks in rich countries(which is itself similar to southeast Asian and native American IQ).
The argument is more "there's probably a world baseline somewhere in the 80's, and black countries limbo under it by being in youtube ads asking for money to save the children rather than for genetic reasons". I'm open to the alternative that blacks just have genetically low IQ's, but I want to see the explanation for a common selection pressure on Indonesians and Irishmen but not Bantus.
And I believe the sahara was not a desert when early man crossed it.
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