'Edit Own Content' permission missing in custom entity
If you look at the end of the node permissions file, you'll see:

permission_callbacks:
  - \Drupal\node\NodePermissions::nodeTypePermissions


If you look at the buildPermissions method, you'll see where the rest of the node permissions are created.  

And then in node.module, take a look at node_node_access implementation of hook_node_access. 

Also, see: \Drupal\node\NodeAccessControlHandler and the corresponding Interface class. It seems fairly complex, but both the node_node_access method and the NodeAccessControlHandlerInterface are well-documented and seem like a good place to start for developing your custom entity permissions system.