It's the same article, but the notes and highlighting system thinks they are two separate articles. If I make an annotation on one article and then look at the other one, I don't see my annotations.
Behind the scenes, these should point to the same article and annotations, so that no matter how I access the content, I see my annotations.
I don't know in how many situations this problem occurs. The Ensign/Liahona situation might be the only one, but maybe there are more?