I’m not sure that I’m making sense, but… this is how my vault currently looks:
I have my entire vault synced to my phone (not using Obsidian Sync), where in the About->Override config folder option I have set it to .mobile. There are two copies of the leaflet folder, one in each, and they currently have no way to sync.
I thought this might be possible because if the user created a folder inside the current vault, the plugin would be able to access it the same way it can access any normal folders, like 5E or Brainstorming in my example.