It also fails to take into account the increase in outside causes of genetic mutations, especially exposure to radioactive elements. As tech advances, more dangerous elements are exploited and more commonly. It's canon that Eezo exposure skyrocketed after its discovery and widespread application, with rather extreme mutations being common (usually cancer, but not always). And then there's unmentioned things like variations in solar radiation on different colony planets, the need to create your own protection against it on space stations and during interstellar travel, exposure to novel pathogens or environmental conditions on colony planets that can cause or encourage adaptations... (Paging @arburi more a more expert opinion on Space Hazards here <3)
Then there's the fact that simply being capable of traveling does not people people are going to actually do that. There's the classic "What's holding you back from traveling the world?" "Money." exchange for starters. Most colonies aren't going to have a reason to visit either, so even the people who can afford to travel aren't necessarily going to travel everywhere. You're still going to have your backwaters and boonies. Not to mention, a big part of what the Galapagos Islands such a genetic cornucopia wasn't that they were completely isolated but that travel between them WAS possible, just difficult enough to be uncommon. Isolated areas that could diversify, and then exchange that diversity with other areas! Adapt, travel, adapt again, travel again, etc etc. Sounds a lot like the great distances between colonies, huh?
And then most damning of all, you have the Unification War. Turians colonization created such isolated communities that they became culturally differentiated to the point of rejecting all outsiders. It's a HELL of a lot easier to export a unified culture than it is unified genetics (see: americanization of media), and failed that? The Hierarchy had to make a massive concerted effort to prevent the natural isolation of colonies from bringing about a second Unification War... But somehow have so much inter-exchange that they homogenized their genetics on accident? Pull the other one, it's got bells on it.
This feels more like a 90s or 00s era rejection of the 80s scifi/futurism trope of racial isolationism than anything. Which, funnily enough, was originally inspired by realworld observation of the results of INCREASED immigration to other (western) countries. People would take advantage of the increased ease of travel, find themselves cultural outsiders in their new lands, and seek out others of similar cultures to consolidate social/political/economic power on a small (city/town/neighborhood) scale. Which was how you got regions of cities referred to as "Chinatown" or "Little Italy" or the like. It's easier to live your day to day life if you are surrounded by people who speak your Mother Language and remember how the Old Country did things, and a hell of a lot harder to get hatecrimed if there's hundreds (or thousands) of people like you in the area than if there's just a couple. And even then, 80s scifi also included a lot of ethnic and cultural mixing as a counterpoint to that, often in the same work. In the Cyberpunk 2020 setting, for example, some of the major gangs (Mob, Tong, Yakuza, etc) and Corps (Arasaka, Militech, etc) are very ethnically focused . But at the same time despite being (mostly) set in USA the "standard" language of the setting isn't English, it's Streetslang. "A universal polyglot of English, French, German, Japanese and a half dozen other languages". Plus, Kimiko Sanchez wasn't named that on accident. =P