Sounds good, but I think you could run into an issue: Allowing real things to overlap could be a bit against physics (so players could not get it). What about thinking about "real" objects beeing distinguishable from real real objects. Like glitching or having a special shader. Than the player knows, which objects can overlap and does not try everything...
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Like the objects which cannot rewind in Braid! That's the issue. I gonna add a new mechanic called delete. It's like the different layers in Photoshop. I could use this for creating a new road. And I think your advice is so great because the puzzle game needs aha and narrow down. If players try everywhere, that's definitely a failure design. Thank you so much!