Select deep structures/cerebellum in script

In order to use the AAL3 regions as scouts, you should compute a volume source model and use the AAL3 parcellation as a "volume atlas". You don't need to add the cerebellum to the surface for this, what you is discussed above and this new menu I implemented are off-topic. Do not try to use volume parcellations as scouts on surface-based source maps.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

Is there a particular reason why is it preferable to create the surfaces from the volume atlas lpba40 or not?

LPBA40 includes a single region for the entire cerebellum, making it possible to use it to create an envelope surface for the cerebellum easily, which was your initial request. But this is not adapted for scout analysis of source maps.