'He only has access to published fares'
Very incorrect statement. Flight Centre has massive buying power with the airlines and as such has 'nett' deals which your mate will have access to. If he doesn't know about them, he's doing his job wrong
Plus if you find a fare by an OTA which is cheaper, it may be a nett fare that they have negotiated and can only be priced and ticketed by them - so you may find a cheap fare for someone but they would still be restricted by where they could book it.
How would you book the fare? You wouldn't be able to book an OTA negotiated fare anywhere but the OTA site - and as such they would include their own markup but a fare would show on the ticket, excluding your mark up - so you'd have to explain that, which can lead to some dodgy territory.