Both are correct, but they have different meanings. English is full of wonderful subtleties! You are really beautiful. (‘Really’ is just an intensifier. It means ‘You are very beautiful’) You really are beautiful. (Here ‘really’ confirms that the statement is true. It’s real, not pretend) An example: A to B: You’re beautiful. B to A: You’re just saying that to make me feel better. I’ve never been good-looking. A to B. No, I’m not. You really are beautiful. The ‘really’ here is to emphasize the truth of the statement.

DavidK gave an excellent answer.

same meaning

They are not similar. You are really beautiful ( is correct)