Running the compiler twice (first in preprocessor mode), then in actual compilation mode is exactly what is done now for many build systems. The first pass, in addition to building dependencies also generates the mapping from files to modules. You will need to list all the files you need to 'preprocess' in your build script, to generate the dependencies, but that's what it is done today already and I don't see a way out nor even a need to change. Modules are not supposed to enforce a specific build strategy, nor they should.

The standard currently imposes very little requirements on the actual build process, headers and source files do not even need to exist as actual files on a system, so it would be a lot of work to actually introduce these concepts in the standard and risk delaying modules further.

That doesn't mean that there might not valuable to standardize that, but it is another battle and many (I, for example) will argue that a strict mapping from file names to module names is wrong.