Of note is that the reconfig adds (I have been told) several tonnes, so the east west journey from the US, presumably DFW, may require even more seats left vacant. I don't work there and never flown on it, so cannot confirm but it sounded factual.
Prior to the reconfigurations the Qantas A380 MTOW was increased to 572T from 569T. Unfortunately the reconfigurations has added 3T to the Empty Weight, so that virtually negates the MTOW increase but does not result in fewer pax being carried between DFW and SYD.
Did the recent LHR-SYD "research" really leave LHR circa 0600………...
The very early morning departure was planned to avoid the usual 30-45 mins of taxi time in the busy congested evening at Heathrow and thus make the flight time look shorter. The early morning departure was also planned to manipulate the fatigue data,
It had more to do with available slots out of LHR for an 'unscheduled' flight (and to a lesser extent, un-hindered arrivals into SYD) than any desire to match the departure time with the crew's circadian rhythms, even though it was probably a desirable outcome for the crew's alertness as you've said.