This stuff isn't relevant at all to the talk - he never talks about npm or anything to do with package managers but instead how node does imports etc.

But anyways, [2] is at least a problem in many other package repositories. [1] would probably be a problem for many - given legal pressure (vendor your shit, that's the solution). [3] was a bug, not a design issue - no package management system is immune to bugs.

The one thing Java has is that it uses namespaces, which may help with [2] (but barely). [2] certainly has been a problem in PyPI.

Certainly all of this could happen to PyPI. We see it happen with js more, I think, because js happens to be extremely popular so there's a ton of packages for it and it's also much younger (especially node) than others.