Managing node with package managers feels like a a bit of a fools errand at the moment. They are going to be wrapping npm somehow, but when npm can't even do things right..
To be fair, that aptly describe being a package maintainer in general -- you spend all day adding workaround patches so build systems stop doing things the "wrong way".
edit: Where "wrong way" is defined as "differently from the target distro's best practices"
The problem is that there is no single package manager that covers every platform. If you are writing an inherently portable library in node.js, as an author, are you supposed to also provide packages for RPM, dpkg, pacman, brew etc? Or do you expect distros to package every tiny thing?
So in practice there is a niche that npm covers, that wouldn't be filled if we removed it.
On the question of whether the system package manager should wrap npm - the reason why you want to do so is because it lets npm dependency resolution work regardless of how packages are installed. If the system package manager just does its own thing, then next time you do need to npm install a package (because it's a relatively obscure package that's not in your distro), you don't want it to install copies (or worse, yet overwrite) all the dependencies that you've already installed by other means.
The usual way package managers do this is, at packaging time, to use the native build tool to install the software rooted in a temporary directory, then fix up those files as needed (including fixing permissions and ownership) and copy them into a tarball. Does pacman not do that?
edit: Where "wrong way" is defined as "differently from the target distro's best practices"