"The boxes are on the shelf."
Translation:Lådorna står i hyllan.
From my understanding, it's that står (stands) and ligger (lies) are more precise and also idiomatic. In English, we say "the leaf falls down" instead of the "the leaf goes down". It's the same kind of thing. Saying är is not incorrect and neither is "goes", but the more precise word makes the sentence easier to conceptualise.