The distinction in the specs and user's guide is between 'ports' and 'headers'.
The two midboard USB2.0 headers give you 3 USB2.0 ports numbers 10, 13 and 14. The other 2 ports, 11 and 12, are on the back panel, making 5 total.
The ROG extension 8-pin connection is not a USB header - no USB ports on there.