I don't see how that's a problem.
By analogy suppose you are simulating a collection of particles following the laws of physics.
For convenience you allow yourself a back door to move particles from one place to another with your mouse pointer.
Do you have to change the physical laws that the particles follow in order to do that? No. The particles can just follow the same laws in the simulation and you can allow your mouse pointer to alter certain variables.
For example if the particles in your simulation are behaving according to the Dirac equation then you do not need to add another term to the Dirac equation to allow for your mouse to drag a particle to a different location. Indeed that would be a very inefficient way of achieving this.
If someone asks does the mouse pointer obey Lorentz invariance then the question would be meaningless because your mouse pointer is not part of the simulation.
If you ask "how far apart is particle A in my simulation from particle B in my simulation?" then you can get a sensible answer. If you ask "how far is my hand from particle B in my simulation" it makes no sense because your hand is not part of the simulation and yet it can make changes to the simulation.
A supernatural force, if there was such a thing, would be like that. The supernatural realm would act according to a different set of rules and our physics would be implemented on those rules just as our simulations physics are implemented on the physics of our world.