ok, since you are using docker, using the jsreport.config.json file will be more difficult to setup..
i'm not sure why the Software Configuration section of AWS Beanstalk is not setting the env vars here but you can try to extend the jsreport docker image and put the configuration there as env vars in a custom Dockerfile.
FROM jsreport/jsreport:1.7.0-full
ENV electron_strategy dedicated-process
ENV electron_numberOfWorkers
# PUT here more ENV calls
then you can upload that Dockerfile and use it for your deployment as described here