It is entirely possible to construct a theory of the universe which states: "All effects are caused by fairies. Each effect has its own fairy, and every fairy is unique. When two fairies produce the same outcome, that is just a happy coincidence." Unfortunately, it is basically impossible to disprove this theory. Also, this theory lacks explanatory power. If I ask the question: "Where will Venus be in 3,000 years?" Fairy Physics can only answer: "Wherever the Venus fairies decide it will be!"
And this is the real problem with Fairy Physics. The problem is not that it is "wrong", because in some sense, it can't be wrong. The problem is that it is useless. And it is useless because it is, in a way, infinitely powerful. It is a theory which allows anything to happen, because it's answer is always: "A fairy caused that."
And thus, we see that a useful theory is one in which we can separate "explainable" events from "miraculous" ones. There are no "fairy miracles." But if we witnessed Jupiter teleport to the other side of the sun that would pretty fairly violate the Standard Model of physics. A theory actually becomes more powerful the more constraints it imposes on how the universe can evolve. That's because more constraints means a greater ability for us as human beings to predict the future.
Physics has proceeded by imposing ever more detailed limitations on how the physical world is predicted to behave. A universe in which quarks and leptons differ across space and/or time has fewer constraints than one in which quarks and leptons are identical. And thus, a theory which describes such a universe is weaker than one which forbids it, because it allows more behavior.
The nice property of a constraint is that it gives you a way to invalidate a theory. The more specific and precise a prediction, the more ways it can fail. And if a prediction succeeds, you thus have more confidence in the prediction under tighter constraints. Fairy Physics is "true" because it cannot be falsified. But such theories are, as we have established, utterly useless. We want a theory with the tightest possible constraints we can impose, because such a theory offers the sharpest predictions and the most opportunities for falsification. If observations are then compatible with the resulting theory, we have much greater confidence in it.
The Standard Model is widely accepted because it offers the strongest possible predictions we know how to make, and our observation of the universe does not provide any strong counter-examples to falsify it. Standard Model-- with bespoke quarks and leptons elsewhere in the universe is a weaker theory, and also unnecessary. So why downgrade to a Ford Fiesta when you can drive around in a Lamborghini?
To give a more explicit example, consider MOND: Modified Newtonian Dynamics. This is a possible explanation for Dark Matter which causes gravity to behave differently on large distance scales. But even this theory avoids letting gravity simply vary arbitrarily across space, because such a relaxation would be giving up too many constraints. An isotropic, homogeneous universe w.r.t. the laws of physics offers the strongest constraints for a physical theory, which is why almost no modern theory will give it up. Doing so cripples the theory to a level that few find acceptable.