I once cleaned up my sister's room. I thought I was doing her a favor but she was mad at me for a week! In hindsight I should have known better. Spacial memory and all that, she knew where everything was even though it looked messy. The article is not talking about the kind of tidiness that is the hallmark of a well-run workshop, IMO. That kind of tidiness is part of what makes more efficiency in that context.
This is something my wife and I have figured out over time - If it's your own space and nobody else uses it, it's fine to descend to 'chaos' because you can just remember where you last put something.
That model breaks if the space is occupied by more than one person, because where one person put something isn't witnessed by the other person. So, having designated places for things and returning them to their 'home' makes the space most usable by multiple people.
Personally, even for solo spaces, I still favor everything having a home because I don't have a good memory for where things were placed.