The same goes for CMSes. Many CMS customers would probably be better off if they took the CMS editor interface as a separate component and wrote the actual page renderer as a custom development separately. The trouble is of course, content systems make it very hard to do that. Having to make things work with the native mechanisms (and the often horrific underlying data model) is what makes huge CMS projects fail or at least perform miserably for everyone involved.
On the very top of the list of abhorrently convolute CMSes would probably have to be Typo3, followed after some distance by Drupal. But the more you work with the initially-liberal Wordpress the more you discover it's not that far behind either.
This reminds me of a bygone era: my startup (now long gone) had its own CMS. Sadly, that wasn't our actual product as we were a pure service company and the CMS was only a tool for us. In hindsight, we should have done it the other way around. Our CMS wasn't perfect, but it shone in a few areas that made the life of both developers and content editors very easy: a simple, accessible data model and an easily extensible page renderer. Unlike many other solutions it was designed to get things done, not to bill a lot of consultant hours. I've yet to come across an open source (or commercial for that matter) CMS that works equally well.
It's about starting to build a specialized system and ending up building a generic CMS because of an urge to make everything runtime-configurable.
"It’s the passion that makes us lose sight of the danger looming ahead, the trap we’re edging towards thanks to our subjective assumptions and vague speculation, the trap of building a overdesigned and overcomplicated system for its own sake. A CMS trap"
and, to address your objection:
"When you are asked to build an app with something like Drupal, you are in a whole different realm, where the CMS trap is pretty much your perpetual state of being."
As I said I would broaden the discussion even further. Over-design and over-complication is very much the hallmark of pretty much any CMS I have come across. The system becomes the biggest hinderance in respect to the realization of content and functionality. This IS pretty much what the article is about. It deals at length with unsuitable customization decisions.