I think you either didn’t mention some requirement, or are too focused on “I need to run scripts to do these updates” because that’s what you use now.

To do “sometimes, I have to update the docker-compose.yml on the unit, or add a library, or change something outside of the unit.”, I don’t see what else than git pull you would need, if you put docker-compose.yml and the libraries in the repo.

rsync or other sync programs also should work.