I think it's easier to understand if you rephrase it as "evolution doesn't encapsulate." Just because a bunch of smaller proteins fold into a bigger quaternary protein structure doesn't mean that those smaller proteins become "private" members of the new protein "class". Any chemical binding sites that are still exposed on the surface of the complex protein will still be chemically active and affected by evolutionary pressure. Even if you have a protein A made up of B, C, and D that all evolved together to metabolize fructose, an exposed binding site from protein C on A can still effect some completely unrelated biochemistry. At the same time, protein C could also be a critical component of a new protein E.

If the evolutionary pressures on E (or C individually) are greater than on A, C could evolve completely out from under A to the point where A is no longer functional or foldable. As such, evolution can't "rely" on abstractions like "protein C" because their "source code" can be changed nonlocally and their function is dependent on very local conditions like temperature, pH, and surrounding molecules. Abstracting away g(h(i(x))) as f(x) in Mathematica is pointless when your packet sniffer can arbitrarily change the meaning of "h(x)" to "nop".