Mmm, I don't agree with your analogy. Yes, you can model things at a higher level, but surely that is for efficiency, not because the model breaks down, in terms of accuracy.
In contrast, there are phenomenon which we know standard particle physics and quantum mechanics gives the wrong answere (despite getting so much else right).
higher-level models are not just for efficiency (though they are mandatory for that: quantum mechanics is intractable to solve directly for even a carbon atom). They also are important for understanding. These two problems are much bigger in terms of applying the standard model for the purposes of 'explaining everything' than the problem of the edge cases it does not explain accurately even in principle.
In contrast, there are phenomenon which we know standard particle physics and quantum mechanics gives the wrong answere (despite getting so much else right).