We would like to generate our JPA meta-models in a separate subpackage to keep our model package tidy. Brief code review of metamodel-generator suggests it ought to be fairly straightforward to add a configuration option that gets passed to Context to provide access to the option at model generation time. I have a patch worked up that I can offer as a PR to move things forward more swiftly if you'd like.
I believe the PR is consistent with the contributing guidelines that I reviewed before submission, but it's quite possible I missed something. In that case I'd be happy to reformulate. Thanks for considering.