I don't think these arguments are valid. For 1) you can always limit the URLs you use to hosts like jsDelivr or unpkg and reference npm packages directly. In this case instead of trusting only npm to send you the code you requested, you're now trusting the CDN as well. Potentially even better could be to import scripts from Github directly. For 2) a simple solution could be to have a deps.ts file for your project where you import from single-version URLs and export the dependency version-unaware. Now your versions are not scattered throughout your application code.
To me URLs seem like a nice (because compact and universal) interface for dependencies which allows decoupling your package management from your runtime.