or you don't use a package manager where anyone can just publish a package (i.e. use your system package manager). There is still some risk, but it is much smaller. Like, if xz were distributed by PyPI or NPM, everyone would have been pwned, but instead it was (barely) found.
It's true that system repos doesn't include everything, but you can create your own repositories if you really need to for a few things. In practice Fedora/EPEL are basically sufficient for my needs. Right now I'm deploying something with yocto, which is a bit more limited in slection, but it's pretty easy to add my own packages and it at least has hashes so things don't get replaced without me noticing (to be fair, I don't know if the security practices of open-embedded recipes are as strong as Fedora...).
it's muddying what a package is. A package, or a distro, is the people who slave and labor over packaging, reviewing, deciding on versions to ship, having policies in place, security mailing lists, release schedules, etc.
just shipping from npm crap is essentially the equivelant of running your production code base against Arch AUR pkgbuilds.
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