Not being in uniform does not mean they were not tech crew heading to Melbourne to operate flight. They would very well have the required uniform apparel in their carry-on bags.
Perhaps they were on standby for this flight (as passengers) and QF was waiting until the flight "closed" to see if some J passengers were no-shows and the non-operating tech crew would be accommodated without needing to downgrade commercial passengers. But by they were required to board, all J passengers had boarder so now someone had to make the decision to downgrade 2 passengers so the tech crew could board. And that may have been cause of the delay as someone with the authority to re-accommodate two passengers form J to Y had to be found, determine who was going to impacted and make the adjustments.
What we do know if that it was poorly handled by the ground staff, but was handled as best as can be expected by the cabin crew.
It is quite likely that this was a legitimate requirement for two tech crew (aka pilots), who are both entitled and expected to travel in J if dead-heading to another port to operate a flight. The issue here is not that a particular AFF member was downgraded, but the process by which is was undertaken and communicated to them.
@Pushka , have you received a points refund yet? Any other communication from QF since the flight?