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..
edit: Where "wrong way" is defined as "differently from the target distro's best practices"
Package managers for scripting languages and similar should be left to manage user-wide packages, or virtualenv-wide for webapps.
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.
package() {
npm install -g --user root --prefix "$pkgdir"/usr "$srcdir"/$pkgname-$pkgver.tgz
rm -r "$pkgdir"/usr/etc
mkdir -p "$pkgdir/usr/share/licenses/$pkgname"
ln -s "../../../lib/node_modules/$pkgname/LICENSE-MIT" "$pkgdir/usr/share/licenses/$pkgname/"
}