I believe the file module has a dependency on the user module that it's not specifying. Although I also think I'm missing something tricky about the base Drupal modules (user, system, etc.) and where they get installed?
I have attached the failing test to demonstrate what I'm seeing. I would expect, if I have a Kernel test, and I attempt to install the file module with the module_installer service, I should be able to do that. Why can I not?