Not only evolution as IRL, in the world of Abeir-toril not only gods and the Creator races, but there are Scholars and beings that literally created new intelligent races: Githyanki, warforged, duergar, gnolls, etc.
Add to that the fact that some elves with the blessing of Corellon could change his biological gender when they´re bored and that´s canon in D&D.
And of course...
If we´re still talking about D&D I have to point out that unlike the Tel-quessir could claim the primal war between Corellon and Gruumsh for their heritage and the dwarves claimed to have been forged from the rocks of Abeir-Toril itself, humans had no unifying creation myth. In fact is one of the few races that exist having originated since before written records existed and were frequently considered one of the creator races, and humans are found in almost every world in Abeir-Toril, and many other planes of existence like the Demiplanes of Dread in Ravenloft.
It is canon that the humans in Thay or Mulhorand were first brought to Toril through portals to another world created by wizard rulers of the Imaskar Empire so they also exist in other worlds outside Toril. So the "it makes no sense that a Human population that appears to be very sedentary and not very well mixed in universe appears heavily racially mixed" could be applied to other worlds but not in D&D. Humans, unlike most other races, did not emerge as a whole but rather in several places at once, coming from elsewhere, thereby resulting in its diversity.
Sc:
↑ Reynolds, Forbeck, Jacobs, Boyd (March 2003). Races of Faerûn. (Wizards of the Coast), p. 80. ISBN 0-7869-2875-1.
↑ Brian R. James and Ed Greenwood (September, 2007). The Grand History of the Realms. (Wizards of the Coast), pp. 5, 6. ISBN 978-0-7869-4731-7.
↑ Rob Heinsoo, Andy Collins, James Wyatt (June 2008). Player's Handbook 4th edition. (Wizards of the Coast), p. 46. ISBN 0-7869-4867-1.
As stated before, in a world that a spell could turn you into a woman or where you have Dragonborn, half-orcs, elves or Goliaths a human with more slainted eyes and dark hair or different pigmentation in his skin is not that big of a deal when you are talking with catmen and avian people daily.
D&D may look like a medieval setting, but it´s not a medieval Europe or medieval Asia, It´s a very different fantasy world with different rules, so I do not think the rules of society, ethics and beliefs of the Earth´s dark ages could apply and if you´re expecting to find yourself in an environment akin to the British-dark-ages War of the roses or colonial south-America in D&D in a world so alien to our earth would not make much sense.
In fact, reaching a city full of caucasian humans with weapons and tools made only of steel and bronze, no magic, without women in the army, a church praying to a one and only god, a ghetto full of jew or dark-skinned humans; the only animals on sight are in sight dogs, horses and cats,... That would break my immersion because that does not sound like any city of any setting of D&D that I know of.
Maybe you can find more points in common in worlds like the one of the Witcher, Song of ice and fire, World of Darkness, etc but right now D&D is a high fantasy setting with little in common with our reality.
