Deploying to live and available modules
I think there is not really a good option for this yet.

It's tricky, because you can't just override the config and have those modules enabled since they also provide their config (which would and install/uninstall processes that can't be skipped. In fact, providing config overrides for core.extension is explicitly prevented.

Maybe someone will come up with a good way to do this, I currently don't really know how that should work.