Various packages rely on node_modules existing as a directory with a particular layout, some rely on being able to write into it. Some of the npm alternatives are built to store and manage dependencies in other ways (e.g., keep packages as zip files or other archives and get node to load direct from the zip), and these other mechanisms do not use a node_modules directory, hence compatibility problems.
I think he prefers a python-esque way where they're sort of dumped in a flat namespace (and not in current project directory), rather than the node_modules way where it's recursively a copy of each thing and its specific exact dependencies, all the way down.
There are ways to not use node_modules, by using newer Yarns for example.
> There are ways to not use node_modules, by using newer Yarns for example.
My point was that if you use yarn2 in pmp mode, and you have a dependencies that depends on the node_modules layout being at the same level as package.json, than even if your package manager doesn't not need or use node_modules, it must emulate it so the dependencies can find their files.