At the end of the article, it is demonstrated that this can happen even with strict equality by overriding the getters. Any language with getter/setter support can do this. Operator overloading can be used for even nefarious ends.
The point is that side effects in code are dangerous, and can be used to mislead a reader.
If this happens, it is not the fault of JavaScript. Anyone who writes code like that for purposes other than demonstration or learning is a moron.