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.