Why not? Fanfiction is all about taking the toys out of their containers and messing with them. Why write an AU where Naruto is female? Why write an AU where Naruto is on a different team? Why write an AU where Sakura or Sasuke are on a different team? You can come up with plenty off ipso facto justifications for why such ideas have potential, just as I'm sure I could for making some of the characters in Konoha, a different race. ( Would it change how citizens other citizens in the village in receive them? Would it change their level of prestige or how hard it is to receive that prestige? Would it effect how they are treated by mentor? Or how they are treated on missions? And so on.) But at its core, fanfic exists, especially AU fanfic, because the author had a story and they wanted to write it. Even if a good deal of thought goes into it, even if there is some grand plan, at the end of the day that is the reason fanfic is written. So to dismiss that as "arbitrary" is in my opinion a little foolish.
But it would just be a throw-away line somewhere, with no relevance on the plot or characterisation (being black isn't even noteworthy when you could be blue) and at that point you have to ask: why make the change.
And while you can make it relevant to characterisation, you're importing social issues which aren't there and I don't read fanfiction for critique on society.