As Studio works as a meta-model that doesn't allow partial contribution (if you don't fill a value in a form, it means the value is empty, not "not contributed"), we should be consistent and make sure that extensions produced by default redefine existing ones if with the same id, not only override.
origin of the demand:
Sometimes, a user needs to override the previous definition of a document type defined in Nuxeo, like Workspace or Folder: for instance, he will need to redefine the accepted document types.
But because of the default definition and the merge policy of the extension point, you can only add accepted document types.
It would be interesting to add a checkbox to force the overriding and generate a contribution like
before the contribution corresponding to what was defined in Studio UI.
Otherwise, we can think about implementing the deniedSubTypes attribute, but it won't solve all issues.