So, I understand that for .onion sites it can help keep them anonymous but is there much of a difference for the user? Does have any added privacy/security?
Connections to clearnet sites have to go through exit relays. While it is wrong for them to do this and they'll get removed from the network when caught, exit relays are in a position to log and modify traffic (HTTPS mitigates this for the most part, but not entirely).
Onion services do not use exits and are end-to-end encrypted. They don't need HTTPS for its encryption and its impossible for connections to be man-in-the-middled.