Thanks for the help; I came to an understanding of how the Java 12 + Beryx Badass Runtime plugin interact.
The Runtime plugin does enforce the use of jmods in the JDK folder but it has a reason to do this: this allows the plugin to adopt a simpler pattern for building different platform's Runtime images. That is; the Runtime plugin switches only the JDK folder per platform; and relies on convention for jmods: no separate config for that.