I believe the ports are just the physical connections to the box. Your adding a hub to one of those ports will expand the number of connections available.
That being said, the rest of your logic sounds fine to me -- a newer hub that is backward compatible. Only thing that may be an issue is that you may need to configure the MoBo for the appropriate port mix -- 7 V1, 5 V2, 3v1 and 2v2, etc. Should be covered in the manual.
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