I think this sentence should come at the very beginning of the course
Put (past tense) not puts
"Who placed this book on the desk?" Is this also correct?
Wouldn't "Who set this book on top of the table?" also be an acceptable translation?
Why atas in this sentence
Atas means above. The book is literally above the desk. Atas can mean anywhere above the desk, whether on it or further above. What matters is you are able to locate it when you look, based on the directions given.
Atop is sama dengan on top