Hi Luo,
Question #1
You should always use MDMGX. Mixing MDMGX with other capabilities like file upload might confuse your end-users since they need to work with different technologies. W.r.t. missing attributes, you could of course enhance the data model in MDG-F according to your needs and include the fields in MDMGX and its inbound processing, too.
Question #2
No, MDMGX does not keep track of extractions or data changes. Nevertheless you can define the extraction criteria in a way that the resulting file contains only your changes. But as mentioned above, you should never change any record that is centrally governed by MDG-F outside of MDG.
Best regards
Michael