Rebuttal from the article's comments worth reposting here -

Mostly, it seems to me that this article argues against a position that very few, if any, physicist really take: it is a composite of extreme sounding ideas from very different sources. It paints the community of physicists, even theoretical physicists, with too broad a brush, by talking for example about "the fashion" in theoretical physics as if all theoretical physics was strings. And whichever their metaphysics, an overwhelmingly majority of physicist accept the confrontation of predictions with experiment as the ultimate arbiter of scientific models. When people calculated the electron self-energy and found a divergence they didn't claim it was actually infinite; they searched for a way to measure it, and for a theory better theory to predict it.

There were some interesting points on taking equations as reality. But I think in fact, the reification of the mathematical structures of Hilbert spaces, state vectors, and hermitian operators occurs precisely when we ask things like "what in the wavefunction is waving?". Confronted with a concrete proposal for a model (some kind of aether, perhaps?) that can generate testable predictions, physicists will be happy to test them. But when done in such a way that there is no consequence to the answer, physicists will mostly don't care. If I pledge myself to a many-worlds, or a Copenhagen interpretation, the transition probabilities or expectation values I compute will remain the same. How can we, even in principle, tell the difference?

Lastly, the two-slits experiments are not ambiguous pangolins that we struggle to accommodate; we understand when an electron will be a wave, and when it will be a particle. Both come from the same mathematical structure; it is not so much a matter of mystery but of counter-intuitiveness, of shattering of expectations. We believe a thing has to be one of the other; but experiments show that is not true, so we accept that's the way things are. Theoretical physicists may ask: "what would it be like it they had to be one or the other?", and the answer is, not at all like it actually is, in very specific ways, like atoms would not be stable, and so on. So we conclude that, even if at human scales things seem to be either particles or waves, in truth they can be both. That's not a neurotic, ever-refining categorization. Rather, it is the merging of categories when they are shown not to be different after all. What produces a crisis is the rigidity of arbitrary categories, when new facts cannot be fitted in then and are therefore put in a special bin. A pangolin threatens your world view until you understand what makes it a mammal and why it belongs, unambiguously, to that category, even if you have to change your category a bit because you realize that it is not scales that make lizards, but some other characteristic, like a quadrate bone in the skull.. Science successfully proceeds in this way. (Why don't we care so much about renormalizability as we do about predictability? Because we transformed our categories.)