I believe that the suggested best practice is to use the Forms module operations when dealing with XFA based forms.
If I remember right, when you use the FSI to extract data, you always get it in the XFA format (with the xfa namespaces intact). This always happens no matter if you have bound your form data to a schema. As I understand it the FSI was primarily built to handle the older Acroforms templates.
With the Forms process form submission you get the data in the correct format. Also server side script can fire, which I don't think happens with FSI.