It might be widely held, but it is not central to Darwinian evolution. (IOW it's a straw man.) Darwin's theory predicts that, e.g. organisms permanently living in dark caves will lose eyes as it's not worth the energy to continue producing eyes, and so those that lack eyes will have a slight survival advantage. Indeed, cave-dwelling sightless salamanders and fish are known, and this is taken to support, not refute, Darwin, even though it represents an example of simplification-through-evolution.
The article is so badly written that it contradicts its "widely held" claim just a few paragraphs later. Genome simplification is widespread, even if this instance is larger than expected. The human genome is also smaller than expected.