EC2 Pass Environment Variables Via "runInstance" to Docker without overriding UserData

I have a launch template (CloudFormation) and a Java App using the SDK. The launch template includes UserData for retrieving and starting a Docker container, but said container expects some environment variables. These I plan on sending alongside with the runInstanceRequest from the Java SDK, but cannot use the UserData for transmission. Any idea on how this scenario can be resolved?

Source: Docker Questions