Everyone is using the same map data, so don't expect much difference there. The benefit of a factory system is full integration into the dash, a clean look and less tendency for theft. (I'm hearing that portable GPS units make an enticing and easy target for crackheads armed with a brick.)
However some factory systems disallow certain features when the car is moving. I'm not sure what Hyundai's policy is. Aftermarket systems have no limitations against entering a destination while moving, but some factory systems do, for example.
Since the only Santa Fe I have driven did NOT have nav, I suggest you test drive one with nav and see how the interface seems to you. And be sure try it out while the car is moving, too. I don't think Bluetooth is part of the deal.
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