I don't have any experience with pipx and personally prefer to just skip the .toml and place the whole pyprojectsetup in setup.py.
With that method, I would write inside setup()
packages=find_packages() # Include every python packages
package_data={ # Specify additional data files
'yourpackagename': [
'config/*'
etc...
]
}
This would however require you to have a package folder which all your package files/folders are inside, meaning the top level repo folder should not have any files or other folders that you want to distribute. Your MANIFEST.in looks fine.
I don't believe the system is that granular. If you're posting in a community that is now hidden I would recommend you to subscribe to it if you want to continue to see it.