I'll back this up with the example of Magento 1. It's a PHP e-commerce platform that has (at first glance) some of the cleanest code you'll ever see in PHP. It looked like the entire development team had come from a Java background. Every component was neatly divided into a PHP object with documented private and public methods. There was a clean MVC separation, with lots of shared behavior abstracted into "Helpers", and a Theme system handling the rendering of the front-end. I have no doubt that the authors of Magento prided themselves on how clean their code was. For them, having spent full-time careers structuring all the many features of their platform into these files, it probably did feel like a clean organization. And when I initially reviewed the code to evaluate using Magento, I also thought it was clean and was part of my choice to use it.
The problem was that when you take something as complex as a full-featured e-commerce system and modularize it so thoroughly, you end up with a literal 7000 classes, and it becomes impossible to figure out the sequence of execution of a single page request through that massive tangle. Is it "clean code" if I have to add debugging print statements to 57 source files to figure out the path of execution that renders a single page?
If I had to choose a circle of hell where I would edit Cyrus IMAP (the worst C code ever) for the rest of eternity, or edit Magento for the rest of eternity, I think I would actually choose Cyrus.