We already have the absolute best method for accurately predicting the world, and it is by experimentation. In the protein folding case, it works by actually making the protein and analyzing it. For designing airplanes, computer models are no match for building the thing, or even using physical models and wind tunnels.
And despite having these "best method", it didn't prevent progress in theoretical physics, theory and experimentation complement each other.
ML models are just another kind of model that can help both engineering and fundamental research. Their working is close to the old guy in the shop who knows intuitively what is good design, because he has seen it all. That old guys in shops are sometimes better than modeling using physics equations help scientific progress, as scientists can work together with the old guy, combining the strength of intuition and experience with that of scientific reasoning.
And despite having these "best method", it didn't prevent progress in theoretical physics, theory and experimentation complement each other.
ML models are just another kind of model that can help both engineering and fundamental research. Their working is close to the old guy in the shop who knows intuitively what is good design, because he has seen it all. That old guys in shops are sometimes better than modeling using physics equations help scientific progress, as scientists can work together with the old guy, combining the strength of intuition and experience with that of scientific reasoning.