Overlapping was used in Tomb Raider III[2] to create a UFO that is larger on the inside than it is on the outside. (This had the unfortunate outcome where I was once killed by an enemy that was inside the UFO while I was outside, but the game thought we were in line-of-sight.) The original Tomb Raider games also used a trick to make the environment dynamic. When they needed to show a wall moving, or ceiling collapsing, or a room being filled with water, you'd be instantaneously teleported to a different map. Sneaky camera positioning made sure you never saw the change taking place. Teleporting is a common technique to make a map appear larger or more complex than it really is. One I learned recently is in The Witness[3].
The best example of a game built around physically impossible spaces is Antichamber[4]. You might enter a room, walk around a pillar, and exiti the same door but end up in a different place than where you started. Antichamber uses portal rendering to show areas that are larger on the inside than the outside, similar to the overlapping in "5-D Space". But also I think it has some teleporting.
[1] https://www.lhowon.org/level/marathon/30
[2] https://www.tombraiderforums.com/showthread.php?t=166545
[3] https://old.reddit.com/r/TheWitness/comments/47pr3h/spoilers...
* Hyperbolica - https://store.steampowered.com/app/1256230/Hyperbolica/ - Allows you to navigate a non-euclidean world. Good luck staying oriented.
* Miegakure - https://store.steampowered.com/app/355750/Miegakure/ - Not yet available, but the videos are interesting. You navigate in a 3d'ish space, but can also modify time.
* echochrome - https://en.wikipedia.org/wiki/Echochrome - What is real in this world depends on how you rotate it. A bit similar to FEZ (https://store.steampowered.com/app/224760/FEZ/)
https://www.youtube.com/watch?v=QTc-rG-nunA ("The Quest to Build a 4D Rubik's Cube")
I can easily imagine a 3D twisty puzzle which allows self-intersection. (To be less cheesy, you could make the self-intersection an objective of the game, perhaps "same color cubes will combine into one cube when they intersect" and then trying to accomplish a final target 3D model.)
I cannot imagine a computer simulation being more robust than reality without relaxing the rules of the physical world (like exclusivity of space/extent). Perhaps something like the Banach-Tarski Paradox[0], where a mathematical sphere can be split into two identical-to-the-first spheres?
[0] https://en.wikipedia.org/wiki/Banach%E2%80%93Tarski_paradox
"Moncage is a stunning vignette puzzle adventure developed by Optillusion. The game takes place inside a mysterious cube, with each side of the cube housing a unique world: be it an old factory, a light tower, an amusement park, or a church, etc. At first sight, they may seem random and unrelated, but upon closer look, you will become mesmerized by the subtle and intricate ways of how these worlds connect."
[0]: https://apps.apple.com/fr/app/quadratis/id1598700673
[1]: https://swissmaprs.ch/wp-content/uploads/2022/11/ParlierTurn...
The Megaminx puzzle is a dodecahedron, having 12 faces. Would it be possible to make a similar puzzle for an icosahedron? What about the stellated polyhedra? Or semi-regular polyhedra? There's no reason we have to stick to the platonic solids, right?
I'm no expert in 3d geometry or twisty puzzle manufacturing but maybe this helps?
https://store.steampowered.com/app/61600/Zen_Bound_2/
https://www.nintendo.com/store/products/zen-bound-2-switch/
possible in a physical form? certainly, but you would never know how much the sculptures are painted: The scoring would be completely impractical for a physical version