I've heard speakers using that very expression ("Says you") in response to a compliment, which makes it closer to saying "Look who is talking" or "You're the one who deserves it". A quick search, though, only led me to the meaning "that's only your opinion" in an expression of disagreement or denial.
If you’re Australian then yes definitely, other regions maybe not. ‘Says you!’ In response to a compliment or insult is effectively reversing the insult/compliment, and is similar to saying “that’s rich coming from you” but without the inherent negativity.
However, “says you!” is interpreted in different regions to mean “so says you” or “you say that (but I don’t)”. So be careful where you use this because the meaning appears to be highly regional.