Have you seen the "mapGenericFilesToLinux" settings  (https://github.com/sbt/sbt-native-packager/blob/master/src/main/scala/com/typesafe/sbt/packager/GenericPackageSettings.scala#L62)?   

In our architecture we try to group settings into three pieces:

*  `raw` settings (configure JUST docker things)
* `Mapped from universal` settings.  i.e.  given mappings in Universal and name in Universal, create a Docker package
* `Mapped from base project` settings i.e. given a standard sbt "application" project, map its files into `mappings in Universal`.

I think you want/need the first two settings for docker.  In other words, I think you want:
*  a `mappings in Docker` setting people can directly assign files *just* for Docker.
*  a separate task that creates the "metadata" files for docker (not the mappings task, which users should be able to modify/replace).
* A separate bit of settings (`mapGenericFilesToDocker`) which take `mappings in Universal` and move them into a Docker friendly `mappings in Docker`.