Balls have all sorts of behavior that goes beyond the typical X-Y coordinates implemented virtually. They spin and slide across the playfield with all sorts of varying degrees and forces. Their motion is very 3d even on a 2d playfield - a moving ball can have a spin axis aligned anywhere on its sphere, and spin at any rate compared to its horizontal motion, and recognizing and handling that is very much a component of advanced play.
Flippers and kickers also have immense subtleties to their behavior. One that no simulation yet gets right is the softness of the rubber on the flipper - balls sink into that rubber by a fraction of a millimeter, and rebound in different ways based on that. Besides that, there are tons of details about how the flipper accelerates and decelerates on a time scale of milliseconds, that an experienced player can feel on a real machine.
Timing also matters. Flipper inputs on a computer are almost always constrained for input timing resolution by the host hardware and OS platforms, typically to a 1/60 second frame rate. Real machines respond hard real time instantly, in under 1 ms. This matters quite a bit too for the degree of control you have over the game.
And of course there's nudging a machine, which has infinite degrees of freedom for direction and intensity (push, slide, shove, slap) that can't be replicated by any virtual controller.
Virtual machines may be infinitely move variable and compact than any physical table, but nothing beats the real thing.
You can start down the rabbit hole at www.pinside.com
Have you tried it in VR? With free head movement, and proper 3D sound simulation, the physics feel a lot more real.
It's still missing good haptics. I think the PS5 DualSense force-feedback controllers and trigger might be able to give you the feeling of the ball rolling around different places, but I don't see anyone trying to make this work in virtual pinball yet.