There is no complete and "bullet proof" simulation of any system as complex as a whole rocket. Every simulation relies on simplifying assumptions, without exception.

Yeah. Most simulations are highly simplified toy models, and most of them need to be calibrated to real-life experimental results. The more complex the system, and the fewer experimental results you've got, the less reliable any simulation is going to be.

WRT Starship, I'm sure that certain aspects (like heat shield performance) can be simulated to acceptably high fidelity, but the entire system is beyond simulation. An accurate simulation would have to simulate the materials and mechanical behavior of every component, in an interconnected way, under a wide variety of stress states -- which is basically impossible with modern technology. Maybe in a few decades...