The fact that npm packages and modules of your application have different naming (package vs module) doesn’t make them different, in fact the more your modules will resemble npm packages the more stable your whole system will be, arguably. This creates a root conflict as you’re suggesting the use of index files for packages.

The another problem here is misinterpretation of Ryan Dahl regrets, as it seems he refers to importing a folder as a module if it has index file in it - which (a) can be messy as definition of index file is quite vague (think ts/js/mjs) and (b) inconsistent as it is not how ES modules work. And as far as I know Node clearly moves towards completely dropping CommonJS in favor of ESM, which only means that instead of `import a from './a'` you will (and already should) write `import a from './a/index.js'`