I have a working solution for this.

I did want to point out that another change (in version you are using) was to limit the application to just a single SourceSet, using main by default. You are using a SourceSet other than main - you'd have to tell the plugin that:

hibernate {
    sourceSet = 'threePartName'
    ...
}

If you could test this locally to verify the changes I just pushed[1] work, that would be fantastic.

[1] https://github.com/hibernate/hibernate-orm/pull/5420