There isn’t any documentation specific to Express, most of them are all over the place, I personally learn most concepts incrementally but what made everything fall into perspective for me has to be this readme https://github.com/Shopify/shopify-node-api/tree/main/docs on Node API library, it has vanilla Node and Express examples. The tutorial covers just about everything you need to get started.
But I doubt there’s one such tutorial specific to the CLI app template since this template is always changing drastically, so they presume we know what fits where in most cases (which much like you I found frustrating).