I use notebooks for individual projects for work, so having a pre-set notebook template I can deploy would help a ton with workflow.
I'm not sure what would be the best way to implement it, but maybe a mapping file as below, and someway to read and apply that would be possible. Maybe the option to capture an existing notebook structure as a template would be possible as well.
{{root}}
{{root}},{{sub1}},{{sub1a}}
{{root},{{sub2}}.{{sub2a}}
{{root}},{{sub2}},{{sub2b}}
EDIT: This is actually already implemented in a sense, by using a JEX export of a notebook and it's sub-structure. It allows for notes and sub-folders to be brought over simply by using Import > JEX.