BocoDragon
or, How I Learned to Stop Worrying and Realize This Assgrab is Delicious
The problem with the whole discussion still is, that Ghost in the Shell is a not a good movie to have it in the first place. The whole idea of the Ghost in Shell universe is, that the shell (body) does not matter anymore, it does not even define you as a human anymore. The whole anime was pretty much about this.
For the major her body is something like a puppet, that why she even uses the standard model without personality modifications. Neither Race nor Gender matter, because the body has become so unimportant. In SAC Batou even suggest that she should use a male model next time.
When the whole "it's a cyborg so the race doesn't matter" concept comes up, I totally get it. I think it makes a lot of sense for this particular fictional universe.
But on some level it brings to mind the whole "It's not an underage character because it's actually a 1000 year old demon" excuse.
In canon you have a very good reason to allow it. Outside of canon? I see a lot of real world (yes, political, sorry Oshii) reasons why people would want to select certain ethnicities. And I think that's what people really want to discuss in topics like these. Not whether or not the canon gives a great excuse to allow it.