As a computational researcher, I disagree with this. (though I do agree most fail to understand the role of computational work; and your comment is a great example of this) This is the type of things people say when they want a loop hole to reject the clear consequences of math.
All simulations are limited and do not fully represent the world. The fundamental task of computational science is to limit the complexity of the system enough that simulation is tractable but the details important to the question at hand are reproduced well enough to be meaningful. We design the simulations to test hypothesis.
Of course, simulations can be wrong (in the same way that web lab experiments can be wrong), but we then have to make a good case for what factors we missed that might explain the deviation from reality. If possible, we then include that in the simulation to test if that re-mediates the deviation. Rinse repeat, till we can answer our question.
Of course, simulations make simplifying assumptions. But to the extent they reproduce reality, that demonstrates the complexities they lop off are not important to understand the domain of reality we are simulating. That is not a reason to disregard the whole endeavor.
Driving this process is a nearly religious commitment to falsifying our own work with good “controls.” We poke holes in our theories relentlessly, because that is how we expect to advance our modeling effort.
An Example
A great example of how this plays out in the debate is the intuitive notion that “shared function” caused by a “shared designer” can explain the similarity between life on earth, and specifically humans and chimps. That is an intuitive and satisfying theory. It is rhetorically strong. It is no surprise that many latch on to this explanation of the world
However, as scientists, we have to rigorously test it. You might be at loss on how to test this. Understandable. This is hard to do, and that is why we need clever people to work hard on it. It turns out that we did test this idea… Phylogeny vs Similarity and Function
The summary:
Shared function can explain the similarity between life to some extent (that is good news). However, it is too much of an simplification. We can explain things much better if we also infer a shared history between life (common descent).
Of course neither model explains everything, but that wasn’t the purpose of the simulation. The purpose is to discriminate these two theories of life. And the simulation is 100% successful in this. This is why we say there is strong evidence for evolution (i.e. common descent).