Packaging all files into a single one is a side effect that we don't really care about. If you want to build your app with babeljs, you need to compile all your backend files. Who cares what the output is, if it's multiple files or a single file? As long as it's semantically the same (meaning even __dirname and friends work appropriately), it doesn't matter.
But what you get is really powerful build system (much better than hacking one together with gulp). Just look how small my config is, and now you can add babel as a loader for JS files and it just works. And you get to use the exact same infrastructure for the frontend.
Webpack also handles sourcemaps flawlessly, and you get tons of other stuff like http://webpack.github.io/docs/hot-module-replacement.html.
For example, you get hashed filenames (for far-future cache expiration in the browser) for free (no manifests or runtime reconciliation of names to assets necessary).