Node js and the the package manager are inextricably tied together. Node js provides a local js runtime environment for the e.g. dev time packages to execute. It's also the api for interacting with the filesystem. Somewhere down there, yes, Node js is a web server, but it's kind of 'the' javascript execution environment for building local packages ("plugins"?) against.
The whole ecosystem is built up on javascript. If you're running grunt or gulp or webpack, it's all javascript. When you install packages globally they're put in a global folder. There are exceptions (I'm looking at you Cypress) that have native assemblies instead of js, but by and large there it's js, and it's stored locally. There are some pretty simple conventions (e.g. the 'node_modules' folder and the hidden '.bin' folder inside that) When running npm it feels like passing a one-liner javascript command into node's javascript repl/environment. The .bin commands are ambiently available.
It makes a lot of sense how it's grown organically... why there haven't been efforts to separate the constituent parts... I don't know. At some point maintaining the 'working thing' with <large degree of> complexity is easier than following a more rigorous, provable set of tools. I think it's a culture thing. Probably the same reason most of the problems are fixed by deleting node_modules and re running `npm i`