The point is, it is my machine to break. Apple is more and more deciding that I don't get to do that. It's a choice that benefits a large class of customers, but it's detrimental to people like me.
macOS used to be "Unix, but with a great GUI". It is turning into "iOS, but with a few command line tools".
Yeah, but there's a certain expectation that the tool that you have installed in /usr/bin is a certain version. There's a reason why tools like Homebrew generally do not overwrite built-in tools.
If you just replaced /usr/bin/python with Python 3, you'd probably break all kinds of things.