A VAR in AdddonsPackages in that root folder or in a subfolder is the same in funtional terms for VAM.
You can move them to subfolders for a file manager perspective outside of VAM, I have it like that for types - Looks, Plugins, Scenes, etc - but this will not be reflected in VAM, apart when choosing a filtered view.
If your goal is to have a folder for a scene plus its dependencies, keep in mind that many dependencies are shared by many scenes, and you probably don't want 20 copies of the same Timeline VAR because it's called by 20 scenes. VAM would ignore the repeated packages because VAM doesn't care for folders, but you'd be wasting a lot of space needlessly.
Related thread:
Hey there what is the best way to delete a scene / look? So many scenes seem to integrate themselves deeply into the system so even removing the VAR doesnt stop it and their is residual files if searched. Im on my second VAM install as my first one is SOOOO LARGE That it barely...
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