Surely "thanks for thanks" isn't such an unusual concept is it really?
People who provide great entertainment on stage are deservedly thanked by their audiences with thunderous applause but the, after the applause dies down, the first thing they say to their audience is invariably "Thank you".
Similarly, I wrote a letter of thanks to the staff at the emergency department of our local hospital. I was both surprised and pleased to receive a letter in return from the senior consultant, thanking me for taking the trouble to offer my thanks.
So when someone is thanked by being awarded 'Best Answer', it doesn't seem at all odd to me for them to then offer their thanks for the positive acknowledgement of their post.