Any mathematical model is going to be inherently limited by our understanding of the objects and forces we're modeling. The model "is what it is". Objectivity is a human trait. I start questioning objectivity when the people who draw conclusions from the model refuse to acknowlege or consider the limitiations of the model, or the possibility that the assumptions it's based on may be wrong.
I'm not aware of any such models. Irreducible complexity is a concept, not a "model" per se; it's meaning is the opposite of reductionism. Reductionism says that the whole is the simple sum of its constituting parts; irreducible complexity says that the whole is MORE than the simple sum of the constituting parts. This would obviously be the situation applying to biological organisms.
And this should be obvious: You can't reduce a biological organism to its parts without destroying it, let alone be able to "reconstitute it" again from its parts. This sort of procedure works with simple (mechanical) systems like, for example, a wristwatch. But biological (complex) systems cannot be "reduced" in this way. It is in this precise sense that we observe that biological organisms are, in fact, irreducibly complex.