I've been doing Scrum-driven development for a few years now after working much more independently for most of my career. I understand why managers like it because it at least lends some structure and predictability to what is an inherently unpredictable enterprise. But the author's criticisms of the incentives of Scrum are on point I think. Because the stories are always articulated in terms of user facing features…
In my view the only way to handle this is to make constant refactoring part of the work without telling management. If you ask for permission for refactoring you will almost always get a "No".
If the organization is not sane, that's another thing of course (and often the case, sadly).