During empower I noticed that some low code apps that were deployed through packages were organized in a separated group from the ones created manually. What's needed to create these groups and associate certain low code apps to those?
Well spotted! You can't achieve this through the UI yet. You'll have to assign sections to an app manually in its App.info.json:
Just assign an array of strings to Sections, and it will create those sections containing that app on the home page.
You can find more details in the documentation.