......was told at check in that he would have to clear immigration in Brisbane and go domestic to Sydney despite there been seats on the 744 from Brisbane to Sydney.
Good chance this was a journey booked by an agent not direct with Qantas - although that doesn't remove the possibility that a checkin agent can use some common sense. I have seen this numerous times especially following a disruption when you discover that many passengers are travelling (say) SIN-SYD-BNE when a direct flight departs at the same time!
East-West Loco could probably shed some more light on this.