How to practically enable `-Wmissing-import-lists`?

This does not quite address your concerns exactly, but it is related. I maintain a compiler plugin called om-plugin-imports, which dumps a canonical list of imports that you can copy-paste into your module that satisfies -Wmissing-import-lists. (see the readme)

It could be easily modified to create a plugin-based solution for exactly what you want. i.e. you wouldn’t actually use -Wmissing-importlists in your codebase. You would instead use a modified version of this plugin, which gave you the exact behavior you were looking for (a compile error when there are any missing imports except Prelude).

-Rick