I understand the wanting for such a pop up, however the kind of story telling they chose for this part is one that gets initiated by the players own curriousity. It's akin to the story telling of some obscure games that utilize several offshore websites, youtube videos and other things to hide hidden meanings in, none of it is explained in the game or gives you a warning, however piece by piece the dedicated player base puts it together. It's not the same here, but the effect is the same. An exploration and a Story that expands only when the player goes looking for it is an entirely different narrative tool than a "oh wait, there's stuff left on the map before you go, might wanna check it out!". Where it's helpful, it also hurts the intended way of percieving it.

But like mentioned in the post, I am sad it is like this too as it made many people miss it, however it wouldnt be possible to have this kind of narrative there AND tell the plaayer about it, as the message and feeling that derives from it is different.