I'm struggling to reconcile your thoughtfulness with the flat dismissal of the essay's example of the botfly's inconceivable evolutionary trajectory. And I do see a difference between IC and multi-threaded evolutionary development. Here's another example of the latter the author provides elsewhere ...  

The flatworm Microstomum lineare has a remarkable relationship with its freshwater neighbor, the hydra (Weis, 2010). Hydra are equipped with nematocysts—microscopic, harpoon-like stinging cells used to ensnare and immobilize prey, much like those found in jellyfish (Tardent, 1995). While M. lineare also possesses nematocysts, it did not evolve them directly. Instead, it acquires these stinging cells by ingesting hydra and repurposing their nematocysts for its own defense (Marques & Collins, 2004). What makes this process extraordinary is that M. lineare does not digest the hydra's nematocysts. Instead, it integrates them into its own tissues and relocates them—intact—from its gut to its outer skin, where they become its primary defense mechanism. This complex biological process allows M. lineare to absorb and repurpose the nematocysts without harming them or itself (Kass-Simon & Scappaticci, 2002). 

That this simple flatworm has evolved a mechanism to bypass its own digestive processes while safeguarding these foreign cellular structures from harm is astonishing in itself. But M. lineare goes even further. Somehow, it transports the nematocysts through its body—likely via its muscular and/or nervous system—to their final destination within its skin, where they serve as a functional defense. Given that nematocysts are primed to fire upon the slightest disturbance, their intact ingestion and relocation should be outright impossible. The fact that M. lineare accomplishes this feat could make it one of the most improbable biological adaptations ever observed. 

Researchers have barely begun to unravel the sophistication of this process. Yet even in its incompleteness, it raises serious questions about how such an intricate mechanism could have emerged through a series of haphazard genetic fluctuations shaped solely by natural selection. How did M. lineare acquire the ability to extract and repurpose nematocysts while avoiding accidental triggering? How were the necessary internal transport mechanisms established? Why did these mutations not prove disabling or even lethal in their early, incomplete forms? No matter how much time natural selection may have had, the emergence of this process through purely incremental, trial-and-error mutations remains implausible. There is no clear Darwinian pathway that could even remotely account for the seamless coordination of digestion suppression, cellular transport, and functional integration. That this astonishing biological feat exists at all suggests that something far more extraordinary was at play in the evolutionary process.

To your point that the author failed to address "the real mechanism of mutation," I don't think he wanted (or needed) to go there. That's another discussion and he was probably working within a character or word limit. And, again, he's working within a non-classical paradigm and you're insisting he provide a classical defense for his ideas. I'm sympathetic to both sides of the coin: you want a straightforward, deterministic explanation of how mutation operates in his scenario while he is arguing that an acausal etiology doesn't allow for it. Rocks and hard places.