Dokku maintainer here.
Providing a custom scheduler - like what software such as Flynn or Nanobox provide - is unlikely to happen. Instead, we are going to support integrating with existing solutions such as ECS, Kubernetes, and Nomad. At the moment, we have a few HA options under development which utilize the plugin architecture to provide alternative schedulers for Dokku.
Both methods currently work, though which you choose and how you integrate them with your infrastructure depends on what your needs are. Feel free to join us on Slack/IRC to help guide future development of each integration.
Aside, the Deis support provided to Dokku was fairly minimal, and mostly went to shared tooling (herokuish and some of the app building aspects). There were no other ties between the two projects, and no existing ties between Dokku and Hephy Workflow (though we wish the project well!). We encourage folks to use the best solution to their problems, whether thats Dokku, Flynn, Deis, Heroku, or any other platform.