As a matter of fact _module_ is a pure theoretical concept. The fact that we’re discussing at least two different implementations of modules alone proves that it’s at least more abstract than _file_. It’s certainly not strictly related to Node, plenty of languages (and their associated runtimes, if applicable) have modules. Further, it wouldn’t matter what a specific implementation of modules within Node is, nor would 14 years of experience with Node.
You’re missing the point entirely, perhaps intentionally? If you’re using modules you’re already using a “build step” - code that runs before your actual code. Your “perfectly working paradigm” is only such if you intentionally disregard the core reason for modules: modularity.