The claim wasn't that the system is "unworkable" in the sense that it's causing world hunger or something, but that the system doesn't "work" in the sense that, in aggregate, it's not "promoting progress of the useful arts."

People will certainly use patent protection where it is available to them, but that doesn't mean they wouldn't have invested in those technologies solely on the basis of first mover advantage [0], and the lack of any observed effect of strengthening the patent system and increasing the scope of what is patentable on R&D spending tends to back that up.

[0] ARM would need a different business model, but it's unclear to me that other business models (i.e., Intel's) wouldn't have been just as successful, and wouldn't come with the social deadweight loss of patent trolls highlighted in the article.