The "cathedral" in ESR's essay wasn't proprietary closed source, it was the GNU project.
Not really. From the essay: “I had been preaching the Unix gospel of small tools, rapid prototyping and evolutionary programming for years. But I also believed there was a certain critical complexity above which a more centralized, a priori approach was required. I believed that the most important software (operating systems and really large tools like the Emacs programming editor) needed to be built like cathedrals, carefully crafted by individual wizards or small bands of mages working in splendid isolation, with no beta to be released before its time.”
So the Unix-philosophy small tools that constitute an important part of the GNU project are excluded. Rather, it’s about any programs of significant complexity, like Emacs (and likely GCC) and many commercial products. While the cathedral model doesn’t imply closed source, it implies building “in […] isolation”, rather than in the open. It may or may not remain proprietary and/or closed source.
Linux demonstrated to ESR that complex projects can also be built in the open with many collaborators, and don’t necessarily require the cathedral; which inspired the essay.