In Python's case, as the article describes quite clearly, the issue is that the design of "working software" (particularly setup.py) was bad to the point of insane (in much the same way as the NPM characteristics that enabled the recent Shai Hulud supply chain attacks, but even worse). At some point, compatibility with insanity has got to go.

Helpfully, though, uv retains compatibility with newer (but still well-established) standards in the Python community that don't share this insanity!

I would say the downside of them is that they're known for replacing GPL software with MIT software