... elves and their +2 Charisma. Are all elves born naturally socially smarter? No, but there is a tendency for society to expect them to be somehow socially exceptional, and this creates a proclivity (or greater ability to take advantage of others' expectations). We're not seeing genetic intelligence as much as the basic tendency that society expects, tolerates, and allows. That's why Trolls, which are discriminated against, have lower maximum (and therefore generally lower average) Logic. They're denied opportunities and express as lower logic.
To some extent I agree, but the mechanics don't really follow the logic there. Elves have a naturally higher charisma
potential because they are elves. That Charisma works across the entire game system. My elf technomancer with 8 Charisma gets an Attack program rating of 8 in SR5. The Matrix doesn't care that she's an elf, and, indeed, her icon in no way shows her inherent
elfness. Yet there she is, running with a stupid high Attack rating on her living persona. Modifiers in social situations have their own mechanic, with Qualities like First Impression. Maybe someone likes elves enough to warrant a +1 or +2 dice pool or limit modifier on interactions. Of course, the opposite could be true, and someone hates elves enough to knock dice off the test or adjust the limit for that NPC. Now, it could be that social standing have given elves a naturally higher charisma because the fact that pretty much everyone loves them really helps their confidence and self-assurance, but that bump to the ego still manifests as an actual change.
In the same regard, trolls have a lower logic potential than most because they're trolls. It's a quirk of the subspecies. People don't become less intelligent because society believes they are. There are a lot of very smart people out there that society would deem "dumb" simply because they don't take standardized tests well or outright don't care. That wouldn't reduce their capacity for logical thought at all--though it might lead to depression and other self-esteem issues.
This is not to say that there can't be exceptional members of the subspecies. But that's what Exceptional Attribute represents.
Lorewise, remember that, every 5000 or so years, magic goes through a cycle, where it waxes and wanes. In the Fifth World, Magic waned enough that the subspecies' traits were hidden behind that fact that everyone looked like a normal human. With the return of magic to the world, the subspecies have retaken their actual appearances. Even in Earthdawn, the scholars at one time believed that the Namegiver races were all members of a single species that evolved in different ways. When the Fifth World came about, they were proven right. And then we forgot about it.
Is that racist? Not really. It's simply science. Fake science meant to justify codified difference between races in a roleplaying game, but science all the same.