Since you're using CumulusCI already, your build environment already has Python and the simple-salesforce module set up. You could use simple-salesforce to write the custom settings into the org.
The run_apex_tests.py script in CumulusCI is an example of using simple-salesforce to query the Tooling API which would be similar to interact with data like custom settings.
CumulusCI's build.xml has an example of how that python script can be called from Ant (NOTE: This would require setting up a python environment on each developer's machine):
I think this is a pretty common challenge which seems like it would be great to include in CumulusCI. There are many use cases that could be solved by being able to easily automate the installation of managed packages, deployment of metadata, and CRUD around data and custom settings. It's been a dream of mine for a while and I'd love to work with someone in the community to help create that functionality. Just create an issue in the CumulusCI Github repository.
For a totally different solution to your challenge, there's a reason this doesn't exist yet in CumulusCI. The Nonprofit Starter Pack 3 (aka Cumulus) uses a facade to handle setting default values in custom settings which has proved very useful both for development and build but also for end users. You can check out the source code of the UTIL_CustomSettingsFacade.cls for more info.