Ok so analogous to, although with different consequences to, Jedi after order 66 and the purge.
presumably all these races have a magical affinity, have you considered adding a seventh characteristic for magic use?
but what my original idea was more along the lines of reduced difficulty on some social checks, so a human in a human shop gets 1 less Difficulty on Negotiation checks.
Another idea would be something like the Dressellian Low Tech trait. The non human pc’s are considered unaccustomed to the Human world (think wizards in Harry Potter), gaining increased difficulty on social and technology related checks where appropriate. If however they spend 20 starting xp to represent a life lived amongst humans. That way you can bump up their base characteristics, abilities or xp and balance it.