Yes, there is a difference. 'You are right' simply means 'That is correct' or 'I agree with you'. Here the words have a literal meaning. It's the opposite of 'You are wrong'. 'Right you are' is an informal colloquial set expression which can be used in the same way as 'OK'. It's mainly British, and quite old-fashioned.

I don't believe there is a difference. There might be culturally (I am not British, nor have I read Harry Potter; perhaps it's some kind of sarcasm). "Right, you are" just reminds me of Yoda from Star Wars.