Currently, the .content.xml files are being processed and can have properties / mixins / etc removed.
However, when, for example, versioning a workflow model, you will notice that the structure will be like this:
In .content.xml, you will notice, in the jcr:content-tag, the following empty tag:
This is to indicate that the XML content of that node is in the external file model.xml (in the folder jcr:content, which becomes _jcr_content after mangling).
An improvement would be to process those files also.