Spyder isn't built-in; IDLE comes with Python (unless you get it via Debian, at least), but is not separately upgradable (as the underlying `idlelib` is part of the standard library).

If upgrading Spyder broke your environment, that's presumably because you were using the same environment that Spyder itself was in. (Spyder is also implemented in Python, as the name suggests.) However, IDEs for Python also like to try to do environment management for you (which may conflict with other tools you want to use specifically for the purpose). That's one of the reasons I just edit my code in Vim.

If updating dependencies breaks your code, it's ultimately the fault of the dependency (and their maintainers will in turn blame you for not paying attention to their deprecation warnings).