I am wondering what is the cleanest way to customize the core node edit form fields like the publishing and menu options fields?

They do not appear in the Manage fields tab, otherwise I would be able to organize them using modules like Display Suite, Field Groups, and either Conditional Fields or Field Conditional States as I do with other fields.

I tried with Display Suite extra's Extra fields feature, but it only adds the fields on the Manage display tab, and not the Manage fields as I need.

My current solution is to add standard custom fields to the node, hide the default ones and code the logic in hook_node_presave() for instance, but I do not know if there any cleaner solution?