I'm afraid the URL for submodules always just points to the repository - you can't specify that you only want a subfolder of a repository, in the same way that git doesn't support "narrow clones" in general.
If you can't live with having the whole repository as a submodule, you could always create a new repository that's cloned from boto and then set up a cron job to:
git fetchthat repository into a directory
git filter-branchto update a branch where the subdirectory is at the top level.
- Add that branch of the repository as the submodule. However, that's all a bit fiddly and my preference would just be to live with having the whole repository as a submodule.