@Shopify I have the same problem. Please at least make a good documentation, because with the current one it's almost impossible to set up a new Shopify app without using templates. Sometimes not possible even with the templates, because of problems such as the one in this post.
I'm extremely disappointed in @Shopify over this forced Remix route with CLI, the documentation is scattered, and surface level at best. I'm all for progress but don't close one door (Node apps for example) until the other is fully open; this is the same type of business decision like when they forced us to use graphQL while it was incomplete by removing REST endpoints. It's having real consequences for my business just in overhead for us debugging this Beta (at best) technology, reverse engineering everything that isn't documented, etc. Terrible business decisions, that Shopify has had a pattern of doing for years now.
At this point I'm going to be proposing to my partners to not develop for Shopify until this is better documented, thankfully we always build a headless backend so I can easily interface the functionality with other platforms so I guess we will just have to shift directions for now.