Yes the CLI app is separate and cannot directly act on the profile of the desktop app. You would need to set the desktop and CLI app to sync to the same target, then whenever you make a change via the CLI app they will appear in the desktop app too. Just make sure you run joplin sync once you’ve made your changes.
In theory you can make both the CLI and desktop app use the same profile via the --profile flag, but in practice it would cause issues if both apps are modifying the same profile at the same time so it’s not recommanded.