Okay, they are classified but I don't see that anything in the setup, or pip package management, seem to actually use them. Are they somehow used in actual package management, or just search qualifiers?
You are correct, the classifiers are just search qualifiers.
However, since pip 9.0.0, it will respect the Requires-Python[0] metadata, which can be specified via your setup.py file.
Since PyPI allows only a single source distribution per release, though, this will still not get you separate modules for separate codebases as it seems you originally desired. As mentioned in a previous comment, it's generally preferred to support multiple versions in a single codebase via six.
However, since pip 9.0.0, it will respect the Requires-Python[0] metadata, which can be specified via your setup.py file.
Since PyPI allows only a single source distribution per release, though, this will still not get you separate modules for separate codebases as it seems you originally desired. As mentioned in a previous comment, it's generally preferred to support multiple versions in a single codebase via six.
[0]: https://www.python.org/dev/peps/pep-0345/#requires-python