This confuses me a little, lol.
In my opinion I believe the chests/boxes with the rare items were hidden VERY well in the Amnesia game. I never found one, though I remember finding a small bag of thalers. Just don't remember where. I guess FG designed the chests as easter eggs. Dunno.
i remember them saying that it was originally planned but later completely removed (since their focus on what they wanted to achieve from the game changed at some point in development). i think they just figured since they got it all working, why remove it from the files? some modder could find use for it. i think the same goes for sanity potions, since those were planned and made but were never actually used.