As much as I hate to spoil the illusion, the kludging you mentioned is basically the sum of the natural drawbacks faced in virtually all game design. Whether it's a skybox, an NPC, or a virtual bullet, it's all basically cheating through constraints and illusions.

Great example: Space Engineers, a very popular game in which you can build ships, bases, etc. with an incredible consideration for automation, moving things around, etc. One of my favorites. But the game intentionally (1) limits the top speed of all entities to 100m/s, (2) doesn't actually simulate orbital mechanics despite having planets, and (3) forces you to construct things on a 'grid'. All of these constraints are arguably shortcomings, but they also enable the physics engine to live and collisions to work.

You're asking a lot from an April fools joke from a comic creation team.

Also, what you're asking for is very hard to do with physics engines as they exist now. Simulating a bunch of non-static elements like that is incredibly expensive.