I do agree to an extent. I am an opera fan, and I have been seeing mixed-race casts for decades. I do not know why it bothers me less in opera. Maybe it is something akin to what you alluded to with the unreality of Dickensian London in Oliver!. Operas are so over-the-top unreal to start with that I do not expect reality. A black soprano in a white part is no less accurate than a fat white woman playing a slim beautiful woman dying of consumption.
I think part of the reason I am bothered by Hamilton is that so many of its fans are young libs who probably don't know squat about history and will come away with the sense that something happened that really didn't.
The Daily Show generation goes to Broadway. :-)
-PJ