It's more of a philosophical question really, but are AlphaGo and AlphaFold "producing" knowledge? AlphaGo plays go, AlphaFold predicts protein structure. They are useful tools, but I wouldn't call what they produce knowledge. However, as you say, their underlying models have certainly captured knowledge that we, as humans, do not comprehend yet.

So I would reformulate the observation of the article as follows: we have become extremely good at building useful tools that embeds knowledge that we do not understand.

If I may attempt an analogy, it reminds of Ptolemaic tables: quite useful at predicting planetary motions with some accuracy. What they lacked in understanding, they made up with accumulated data and complexity. Maybe AlphaFold is just that: a Ptolemaic table built on top of a huge swath of data.

We will probably build a lot of these tools in the future, as we have very powerful tools to build them. But I don't think they will replace a more fundamental understanding (that is to say science), that will simply lag behind.