I guess I’m trying to connect the dots on how a simulation improves the actual vehicle dynamics.
Simulation inside the engine can find resonances, show where shockwaves propagate, and show you how to build injectors (pressure, spray etc) so they are less affected by the path of reflections. Optimizing things like that smoothly along a range of velocities and pressures without a computer is not very feasible, and you need a minimum of computing power before you start converging to accurate results. The unpredictability of turbulence means low-resolution simulations will behave very differently.
Modern pressure vessels can reach 5% empty mass, thats a factor of 20
Rockets have stages, a good approximate is to stage half your rocket to get rid of the most empty mass. This also means your first stage has to have double the thrust to lift itself and its stage. Now you're at a factor of 40 just to hover.
Now you actually have to take off, usually around 1.2 to 1.4 thrust to weight.
So a more realistic scenario means your rocket engine has to throttle down to exactly 2% power while the laval nozzle is optimised for takeoff thrust only.
One major reason for this is the mixing plate at the top of the combustor. Fuel and oxygen are distributed to tiny nozzles which mix together. The better the mixing, the more stable the burn. If you get unstable burning -eg momentarily better mixing in one area- it will cause a pressure disturbance which will further alter the burning power in different areas of the combustion chamber. At low throttle, this can be enough to cause the engine to turn off entirely.
Fluid simulations have made a huge difference. It's now possible to throttle engines down to 5% because mixing is much more stable (manufacturing improvements in the nozzles have also helped) and combustion is more protected from pressure variations.
The extra stability also just makes it easier to control a rocket period. Less thrust variation to confuse with drag properties, less bouncing, better sensor data.