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.
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.