The scientific method, whilst very useful, is still the empirical method with certain postulates.

It really isn't. The presumption argument requires that you are a mind reader and can be 100% certain that you know what unstated priors a person is operating under. If they deny them, you mere reassert it. It is a non-falisifable claim. Thus the attempt to disprove science required a return to faith.

Fish do fine and know nothing about water. Birds fly and don't understand aerodynamics. The vast majority of life in existence conducts energy production via ATP and only a small fraction of the human race has understood that. Fireflies don't know that they are doing the most efficient form of light production from chemicals ever found.

The whole presumption apologetics argument is a garbage heap only advocated for by people who value faith over experimental methods. A false attempt to sub in a bad contextualization from the things itself. You don't need to have a fully worked out from first principles understanding of the universe to conduct a basic experiment. It might be helpful, maybe, but it isn't required.