Sorry for the late reply.

I would really like to provide a runnable test case, but I don't know how to do that with your test templates.
There are no templates for metamodel generation issues. I also looked at your test and it is exactly my scenario

Sill searching for reasons why there is a difference between a project and your testsuits.

What I've found:
#The compiler (Eclipse) picks up the metamodel processor and generates entity_.java files, that are incomplete.
#When I build the project with maven and decompile the entity_.class file it is complete!
#When I use maven-processor-plugin instead of compiler it seams to be that entity_.java file is also complete.

I think, the preferred way should be to have processors on classpath and everything works.
The maven-processor-plugin was a "workaround" because of other maven issues in the past.

Finally it seems that the problem is not yours, but I do not really understand, why sources are generated differently
(Eclipse compiler, Maven compiler, processor-plugin, ...) with your metamodel processor.

Thank you for your time..

PS:
The only way to show my problem is to create a new maven-project in eclipse,
add hibernate-core and hibernate-jpamodelgen (optional) dependencies,
create the entity and embeddable from my scenario and you'll see the wrong source file.