A perfect theory of physics that exactly predicts the behavior of atoms doesn't really help you much when you're trying to predict the behavior of a spaceship containing approximately 10^33 atoms. Any such prediction is going to involve an enormous amount of heuristic approximation.

Just as one example, a spacecraft moving through a fluid atmosphere and with fluid fuel/oxidizer burning in its combustion chamber is going to involve incredibly complex turbulent fluid flows. And turbulence is something that we famously don't have good high-level theories (approximations) for.