It's not that packagers are using npm. It's that they might want to package a node application for their distro's package system, and now they have to sift through thousands of npm packages (already a nightmare). They can't just make a system package for every npm package, not just because that would violate packaging guidelines for any reasonable distro, but because one project can pull in multiple versions of a single package. The Nix and Guix crews can handle that (and that they can is as much of a bug as it is a feature).

There is no clean way of packaging a typical node application.

Passing class instances around like that is the real code smell.

Often, yes, but not always. Allowing fine-grained control over performance is one good reason that a library might expose class instances from one of its dependencies.

> Or you could have all the bugs introduced in everyone's hand-rolled implementations of it.

Only one buggy implementation per project. Compare this to including the same library in dozen different versions, because dependencies have their own dependencies. And you can neither track the versions nor update them.