Well, consider that at a certain level there is a more space between matter than anything else, and I think your logic becomes very illogical. In other words while the "analog" world looks continuous and solid, it is not. Again, there is far more space in an atom than there is atom. At a certain resolution the space becomes imperceptible and everything thing seems solid. This is true with digital audio also. I guarantee you cannot tell the difference between 48khz sampled digital audio and analog, unless you can tell the digital by the decreased noise floor.
Further more, a guitar amp is far simpler than any living thing including a flower. It is perfectly reasonable to consider the operation of a physical device such as a tube or resister can be described mathematically to a degree that the digital model becomes indistinguishable from the real world device.
I suggest that the axeII operates at this level. First consider that norm is that not even two "identical" guitar amps sound and feel exactly the same. Perhaps the models in the axe don't sound exactly like your amp but it does sound like an amp; it will have the general essence of the modeled amp. It is as organic as as the real amps I am accustomed to and in many cases sounds better.
As they say, your mileage may vary.