Passing arguments to different kinds of deployments in kubernetes
With Helm, I like to think of the Chart as the function and the values.yaml as the arguments. If you are selectively including and excluding certain ConfigMaps, you are changing the function and will have to have a separate Helm Chart for each deployment. It will also complicate things like updating, since you'll have to update each Helm Chart individually.
Unless there was some strange extenuating circumstance I would just create different values.yaml files for the different deployments. An added benefit is that when you list your Helm releases, you can easily bring up the .yaml file for any of them to load the config.