They may or may not be running Node.js specifically, but I believe that many Linux distributions, as well as Windows, include JavaScript code in core applications. I don't see this as particularly different, except that they might choose to assume a single standard system Python that is able to be modified by standard Python development, whereas I would rarely expect that to be the case with however each component chooses to execute JavaScript.
No, they're not. I'm talking about core apps and services that are essential to a functional operating system. This is exactly the same situation. The difference is choices made by the OS and language ecosystem about how to manage dependencies in various use-cases. It is an apples to oranges comparison because of those decisions and not because of the language.
Python is different here because in many linux distributions, there are many tools that rely on you system python. Python unlike node is not limited (in practice) to web applications. that's why you have to be more careful. So while I understand you are using this as an example, I don't feel that your comparison is apple to an apple.