You can add any folder to immich as external library. No need to use cli.
So if you want custom structure, synchronize files from mobile to server in any way you prefer (Syncthing, PhotoSync, etc.) and add that folder as an external library.
This is quite a basic feature which should be inbuilt to the Immich mobile app. It's a common use case to want your screenshots, WhatsApp media album to not be displayed on the main timeline.
If you're running an instance for less technical users it's more hiccups to setup syncthing etc and have to explain why another app is needed.
So if you want custom structure, synchronize files from mobile to server in any way you prefer (Syncthing, PhotoSync, etc.) and add that folder as an external library.