I think the problem that GP is getting at is the philosophical problem of apocalypticism or market perma-bears, which can be summed up in this satire of them: "So and so is a great market analyst! He's predicted 30 of the last 2 market crashes!" A broken clock can still be right twice a day, but it's still a broken clock. Predictions about the future which are so broad so as to be hopelessly incorrect should not be excused because part of the prediction surface ended up being correct; rather, the entirety of the prediction surface and accuracy should be taken into account to determine the overall accuracy of the prediction.
Taken in that light, his being correct about his protein folding prediction feels like cold comfort when taken in context of his predictions, largely unsubstantiated, of AGI becoming a malevolent human extinction force at par with or of greater risk than that atomic bomb. It elides the very real conceptual limitations of current implementations of AI, such as it's inability to recognizing bidirectional associations (Tom is John's son means John is Tom's father), protecting against injection risks, "hallucinations" (inability to differentiate between when it is making something up and when it is not) and a variety of other existential limits towards its own power.
These details, far from being inconvenient nuances that do not detract from his overall point, should actually serve to make us seriously skeptical of how well he understands the risks of the entity he is warning against. A more skeptical observer might even say (and I'm one of them) that much like fire and brimstone preachers, he is trying to create an unrealistic fear of a deific entity that cannot be reasoned against so that he can consolidate power by serving a "solution" that protects against it and curry popular favor. I find his approach to be the distasteful and manipulative approach of the common demagogue. The haughty, arrogant, insecure way that he treats the arguments of his critics (he simply blocks them on Twitter or condescends to them) make me even more skeptical of him. It makes me wonder if on some level he knows that his argument is not being made in good faith, and isn't trying to win an argument in good faith.