1)All packages that are published can never be unpublished or re-released from a different contributor
2)Packages are namespaced
3)Nobody downloads packages directly from the internet. You always use a proxy which in most companies has security scans.
4)There are no "local packages" (like the node_modules dir), so it is impossible for the checked out source code to override your own vetted and secure package.
Not directly related to the incident of the original post, but I was mindblown when I realized that you can unpublish npm packages