Quantum mechanics (or QFT) isn't likely to be found wrong anytime soon. And if it is, it will be to such a degree that it has almost no day-to-day consequences (much as how GR is only considered for particle physics and satellite synchronization).

What I mean by this is that the whole nature of chemistry and biology is already rooted on a very secure foundation. So as simulation capabilities increase, you can be sure that these have a very high probability of modeling the "higher-order" phenomena correctly. Even superconductors and superfluids can be modeled correctly. The only things that may not be correct would be the high energy limit of quantum gravity models. But simulation in this area is almost (and may be?) nonexistent.

Now... having stated that we have an almost perfect description of the underlying reality for any practical phenomena we would be interested in, it is true that this model is currently mostly unamenable to calculation. The amount of computation required to reach chemical accuracy is very high and we may not have that capability for quite a while. So we make concessions and approximate things. For example, wavefunctions are modeled as Slater determinants which satisfy the wavefunction's antisymmetry but do not take into effect all the correlative effects (like electron-electron interactions).

It is a scientific and mathematical challenge to characterize exactly how much these models are off from the "true" solution. Most of the time, you have a good idea if the approximation you are using will work for your domain. If I want to fold proteins, I don't need anything more accurate than CHARMM (describes pairwise interactions; it's a non-reactive potential). But if I want to study Cooper Pairs (in superconductors) I'm going to need to make many less approximations, and it will be a much more expensive model computationally.

QM says nothing about the validity of your simulation. Worse we are incapable of simulating something as complex as a single helium molicule using the full QM model for 1 second using 1 days computing power on any current supercomputer. Even protean folding is forced to greatly simplify what's going on to the point it's often wrong. ( Proteans are not folded in a vacuum.)

Want to simulate a cell? Even with hardware 10^100 times faster you can't use QM, it's all models of models. None of which are 100% accurate, but that's no reason you can't Kidd yourself.

Am I missing something or did you not read the post you replied to?

From a practical standpoint Chemistry is not based on QM. You basically said QM > Chemistry > more complex things, my counter argument is even fairly simple. Chemistry is way to complex to model from pure QM. So, even at your first step your model is making simplifications. And 10^100 times the processing power does not get you to the point where you can model even the simplest cell for a meaningful time-frame.

Even at the timescales of atomic explosions and the best hardware / software around those models are vary simplified.

PS: That's not to say you can't make useful simulations, but trusting them to be accurate without testing is not science.