Export administration utility only extract last document version and recreates folder / documents estructure.
Migration process converts from older repository structure to newer.
If you want to extract all files to you file system you might create a simply java application via webservices -soap - to doing it. And you might get some decission about how to name the version documents, for example if document "document.doc" has tree version probaly you would like to store older version as document.doc and others like document_1_2.doc and document1_0.doc ( that's the reason why export from administration not creates the version documents, only the last ).
