Your original point was:

> you could not have different versions sitting side-by-side.

bundler can't do that either. You can't depend on both rails 5 and rails 6 in a single package. Most languages can't do that.

> Any project that's lived long enough runs into some sort of version mis-match where the solution is `rm -rf node_modules`.

I agree, but that's not the only solution, as I've said you could write something similar to require "bundler/setup" in JS that does version checking.

> The version of ruby and the version of the gem are explicit allowing separation.

You can specify the node version in your package.json.

EDIT: on the version checking point, I agree that this is a deficiency of npm. It probably should ship something similar to bundler/setup by default and encourage users to do

   require('npm/validatePackageVersions') # or import 'npm/...' in es6

in their top level code.

I was just pointing out that this is not a fundamental limitation of npm, and it should be fairly easy to implement in user-level code