More importantly, we have 0 evidence that using private/protected in software is better than not. People like to use them because, as the author notes later in the Type System comments:
"Refactoring. If I’ve got a type system and I’m faced with needing to clean things up, I can put stuff behind an interface and follow the type errors to find everything that needs updating. Often in dynamic languages, even with a decent test suite, extensive changes can be really difficult."
You shouldn't have a workflow of fix failures blindly and private variables contribute to that style of over-reliance on language features instead of actual attention to detail.
That being said, the world isn't perfect and it's common to take this approach if you have a lot of strong language safety features and are under time pressure (who isn't). In my experience, this situation means things are being rushed and/or the developer is burned out to give up such fine grained control over the code.