"Thus, since you don't know a lot of things, you can't be sure that what you simulated was indeed the real thing or something that you imagined/theorized to be the real thing."

That's a useless distinction as there is nothing where you could "know the real thing", you _always_ work with theories, without exceptions. When you take your first step out of bed in the morning, you don't know the _real_ behaviour of the floor (it's made of atoms, after all), you "only" use a relatively high-level theory of solid materials to predict that it will support you before you step onto it. There is no guarantee that that will work out, but there is fundamentally no way to do better than that, all of science works that way, _everything_ we know about the world is "a theory", even the atom theory is a theory, and the quantum theory is a theory, it's all about modeling as best as we can, none of it is "proven to be the real thing", and no scientist ever even tries to prove something to be "the ultimate reality", all that matters to science is to make models more precise, and to figure out what those models seem to be sufficiently precise to use for - and then use them, which we do very successfully indeed.