That is for
everything required to run an
entire operating system. You're actually putting Node's micro-package madness into even more of a negative light from this comparison -- if it takes only several hundred packages to run an entire distribution, why is it reasonable to require that many packages to run a single web application (not to mention that most distribution packages don't depend on hundreds of others)?
The difference is that the only people looking into NPM packages are the Node community. The entire Linux community -- which includes a large portion of the Node community mind you -- looks into the set of packages you are looking at (yes, we've had a bad rap in recent years -- but in our defence we really are trying).
I'm a little biased with regards to distributions (I work for SUSE), but I like to think that working on a distribution has given me a much better understanding of how much work goes into those packages. I don't think you could adequately replicate most of that engineering in the time that most micro-package ecosystems have been around.