"You really are beautiful!" and "You are really beautiful!" (both acceptable answers) can have different meanings. The former can be said to convince a person that he/she is beautiful or that the speaker is surprised by the observation that the person is beautiful.
The latter can be said to tell the person that the speaker definitely believes that he/she is beautiful.
Which would be the correct way to use "Du er da smuk!"?
I'm not Danish, but I think that would be an acceptable translation if you emphasized it correctly, aloud -- but this is hard to express when writing it down.
The usual interpretation of the written sentence "You are so beautiful" would be that the speaker is gushing over how beautiful you are. But I don't think that is what the Danish sentence means.
I think what is wanted is the idea that you have said previously, "I'm not beautiful" -- and the speaker is contradicting you. They can say this with "You are so beautiful," by emphasizing both are and so. They can also just say "You are so," or "You are too."