Items reverting to their locations disoriented me at first too, but I don't think it was a bad choice. I definitely think it would've bogged things up for me if I had to sort through some 12-odd symbol pieces at the gate part. Coming from someone that instantly picks up anything they can, at least. You might be a more discerning bird.
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I see your point, and now I think it does work well for the symbols on the table. I guess I was mostly confused because the moment I experience this mechanic was when I tried the wrong tool on the trap door but clicked the left mouse button, so the tool just disappeared and nothing happened. It was a good thing that the other tools are at the same spot, so I did notice the first one had returned to its place. A little explanation might prevent such a confusion, though I can't think of one right now that fits the game well. Maybe just a text box saying "The hammer was returned to where you picked it up" when you first drop something. Not very smooth, though.