How to Avoid Empty Folders in Exported Asset Package?

I'm trying to export an asset package containing some prefabs and scripts, but the package ends up containing some empty folders from elsewhere in the project. Steps:

1. Assets -> Export Package...

2. Uncheck "Include Dependencies"

3. Click "None"

4. Check just the root folder containing the assets I want exported

5. Click "Export" and put the .assetpackage somewhere.

When I import the package into a new project, it imports the files and folders I expect, but it also imports some empty folders that are siblings to the folder I wanted to export, including a nested sequence (Standard Assets/Character Controllers/Sources/Prototype Character/Materials and .../Textures).

These folders don't have anything in them after the import. They aren't dependencies of my assets or referenced in my scripts. They do all seem to be empty folders in my original project and don't even show up in the original Export dialogue. I could just delete them from my original project, but this seems like a workaround for some bigger issue with my process.

How do I avoid exporting empty folders from my project every time I export a package?