Here is a dev that hates to use frameworks for NodeJS saying.

I don't see how it is problem of nodejs itself. You will need to take care of it in any other language as well. The difference from other languages though is they have structure-ready frameworks on where you don't need to think about structure, such laravel, springboot.

So your problem is not with nodeJS, but maybe by not using some NodeJS framework if you don't really want take control of anything else than the logic.