My use case is related to this: Workspaces in Bear?
So basically file based storage would help me to completely separate work and personal notes. I could have them in totally different backend sync service even (iCloud vs e.g. Dropbox or OneDrive). This is one of the strong suits of Obsidian or even Craft that nowadays supports local storage (they call it “External Locations”).
I guess there is multiple ways to solve the need for having multiple “Notebooks” but having actual files that you can store in different locations would be one way to solve it.