I think something like an npm diff command would be helpful. This would allow you to see the changes from a previous version that you just upgraded from. This would somewhat replicate the functionality that commiting your node_modules directory to git would give you.

Not sure how that would help. Anyone can publish anything to npm, it doesn't even need a repository. So unless the source code itself was hosted on npm, and the entire toolchain was controlled by npm, there's not much to do.