FYI you don’t really need to create your own container for IS. You can just download prod ready version from containers.softwareag.com. Only MWS is not prepared this way.
For configuration variables, you have 2 options there. You can use the webmethods helm charts and do the configuration on container startup level, or you can push the configuration files to a git repo, and sync it using CI/CD pipelines. Helm is a package repository for Kubernetes and these Helm Charts I linked are also provided by Softwareag and by default they are set to download the container from containers.softwareag.com. You may want to mirror that repo to your own git repo or create your own values.yaml file and inject it during startup. The documentation can be found in the git readme file.
I recommend not putting any config in to any containers. In helm charts there is a values.yaml file where you can make all your changes in one place.
edit: Here is the community post about helm charts.