It seems the plugin is designed to publish to multiple EB environments within a single EB application in a single AWS account. It's not obvious from looking at the sample beanstalk
DSL block on the README how to handle multiple applications or accounts.
I assume it would be possible by using Groovy variables in the build file, but it would be better if there was a standard/documented way to do it with the DSL and standard beanstalk Gradle tasks.