Thanks for reading!
If I'm understanding your counterexamples correctly, the idea is that we've developed technologies from the study of messier "non-isolable" systems. Flight is a compelling example because fluids are notoriously challenging for mathematical description, although of course there is an incredibly succesfull domain of fluid mechanics.
I do, however, think that the way we've developed flight and related technologies is still applying isolable-thinking to non-isolable systems. (Pardon the following incomplete understanding of flight). The basic principles of flight seems to depend on neatly separating processes in an isolable way, for example by decomposing it into separable forces of lift, drag, stiffness, etc. And the technology we get out of it - airplanes - are mechanical systems that necessarily have isolable/neatly decomposable properties. Organisms can fly, and to a certain extent the basic principles apply - generate lift - but the architecture that produces flight is nothing like the neatly decomposable machinery of airplanes.
For a better argument along the same lines I'd recommend Robert Rosen's Essays on Life Itself. He discusses flight and the differences between natural/artifical wings to highlight a similar ontological split between organisms and machines.