I have a Msc in microbio, not biochem, but my understanding is that proteins don't have a constant shape. They vibrate, interact with other molecules, etc.

You won't have a perfect answer unless you want to predict its shape in a vacuum, which wouldn't be very useful either way. Having it "close enough" is already extremely useful. There are definitely edge cases where it gets it wrong, but there are always edge cases in ML. More data = better results with the same architecture.

Tons of things that won Nobel prizes weren't 100% accurate, it's not a prize for solving science, rather a prize for advancing science.

My wife is a neurobiologist and the impact of this advance is groundbreaking for her work.